From owner-chemistry@ccl.net Wed May 26 00:06:00 2010 From: "Jiabo Li jiaboli:_:yahoo.com" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41967-100525224826-12764-cyn5crIZaOSk0BpA6k/20w-*-server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-46328946-1274842094=:80568" Date: Tue, 25 May 2010 19:48:14 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli::yahoo.com] --0-46328946-1274842094=:80568 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable The most likely scenario is the basis set linear dependency. GAMESS remove = the linear dependent (or more precisely, the near linear dependent) compone= nt in the basis set space. This certainly will slightly change the energies= . Here is an example output from GAMESS. You can check your log file for si= milar information: =A0 =A0NUMBER OF CARTESIAN ATOMIC ORBITALS=3D=A0=A0=A0=A0=A0=A0=A0 166 =A0NUMBER OF SPHERICAL CONTAMINANTS DROPPED=3D=A0=A0=A0=A0 0 =A0NUMBER OF LINEARLY DEPENDENT MOS DROPPED=3D=A0=A0=A0=A0 2 =A0TOTAL NUMBER OF MOS IN VARIATION SPACE=3D=A0=A0=A0=A0 164 =A0THE INPUT BASIS SET CONTAINS APPROXIMATE LINEAR DEPENDENCE. =A0THE SMALLEST EIGENVALUE OF THE OVERLAP MATRIX IS=A0=A0 2.898259E-09 =A0THERE ARE=A0=A0=A0 2 EIGENVALUES LESS THAN QMTTOL=3D=A0 1.00E-07 =A0EIGENVECTORS BELOW -QMTTOL- ARE DROPPED FROM THE MO SPACE, =A0IN ORDER TO ELIMINATE THE APPROXIMATE LINEAR DEPENDENCE. =A0THIS WILL MOST LIKELY CHANGE THE ENERGY ON THE ORDER OF TENS OF MICROHAR= TREES, =A0DEPENDING ON THE NUMBER OF ORBITALS REMOVED.=A0 THE VALUE OF QMTTOL CAN = BE =A0CHANGED IN $CONTRL: JOBS WITH EIGENVALUES BELOW 1.0E-07 PROBABLY WON'T =A0CONVERGE.=A0 EIGENVALUES BETWEEN 1.0E-07 AND 1.0E-06 MAY REQUIRE LOOSENI= NG OF =A0THE DENSITY CRITERION (CONV IN $SCF), MORE ACCURATE INTEGRAL EVALUATION =A0(ICUT=3D11 IN $CONTRL), MORE ACCURATE DIRECT SCF FOCK MATRIX =A0CONSTRUCTION (FDIFF=3D.FALSE. IN $SCF), OR CHANGING THE SCF CONVERGER =A0(DIIS=3D.TRUE. IN $SCF). =A0 Hope this solves the mystery. =A0 Jiabo --- On Tue, 5/25/10, Gustavo Mercier gamercier+/-yahoo.com wrote: > From: Gustavo Mercier gamercier+/-yahoo.com Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussi= an To: "Li, Jiabo " Date: Tuesday, May 25, 2010, 3:32 PM Hi! In addition to the many suggestions that you have received I would add: 1. GAMESS direct scf has several short cuts. Look at the control keyword gr= oup for this. I would get rid of it for both programs. 2. DIIS also has adjustable parameters, including how much 'history' you ke= ep. 3. With large basis sets there may be some linear dependencies and the prog= rams may automatically make changes in the basis set. Check your output. Review the GAMESS documentation and check out the fine print. Look at the f= ile "refs.pdf", for example. The developers have made a variety of choices = in the implementation of different algorithms and they may tell you that th= eir choices may result in small differences. However, these can easily be i= n the millihartree or less. You may conclude that getting the exactly the s= ame result is not reasonable. This does not even include such details as co= mpiler flags and optimization schemes used with different compilers. =A0 -- Gustavo A. Mercier, Jr., MD, PhD gamercier|*|yahoo.com Gustavo.Mercier|*|bmc.org gumercie|*|bu.edu 617-414-6440 > From: Piotr Nowak piotrnowak[*]student.uw.edu.pl To: "Mercier, Gustavo, " Sent: Tue, May 25, 2010 1:53:20 PM Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussi= an First of all, thanks everyone for response. Some questions and suggestions = appeared; I'll try to answer them briefly: -I've been using exactly the same structures for the single point energy ca= lculations; -I have been using spherical harmonics in both programs. Gaussian uses them= by default, and I have ensured their use in GAMESS with "ISPHER=3D+1" keyw= ord. The number of cartesian basis fuinctions is the same; -Gaussian manual states that default grid uses 75 radial shells and 302 ang= ular points/shell. I have been using the same grid in GAMESS thanks to "NRA= D=3D75" and =A0"NLEB=3D302" keywords. I also suspected that grid handling m= ight be implemented differently in both programs, therefore I tried some "s= uper-ultra-extra-fine" grid with 250 radial shells and 974 angular points/s= hell (using "Int(Grid=3D250974)" keyword in Gaussian). Unluckily, the energ= y difference remained within the same order of magnitude as it was with for= mer grid; -The relative energies are still different. If you compare e.g. different g= eometries of the same molecule, or activation energies, the error is still = 10^(-4) hartree. I would agree with Soren - there must be some "hidden" adjustable parameter= s, but I have no idea which one can cause these differences. I still hope i= t is possible to get the same results using both programs.=A0 Kind regards, Piotr On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piotrnowak!^!student.uw.edu.p= l wrote: Sent to CCL by: "Piotr =A0Nowak" [piotrnowak~!~student.uw.edu.pl] Dear CCL users, I'm trying to reproduce single point energy obtained with Gaussian 03 using GAMESS US. Hartree-Fock energy is almost exactly the same e.g. Gaussian: -1849.26414782 GAMESS: =A0 -1849.2641478646 Unfortunately my attempts to get the same results using DFT failed. The energy differences between both programs are unreasonably huge. Here are so= me examples of results for different functionals (the same case as above- mentioned HF example): M05-2X Gaussian: -1855.79754118 GAMESS: =A0 -1855.7976587495 SVWN5 Gaussian: -1845.45112047 GAMESS: =A0 -1845.4510666810 Slater (also known as Dirac, one of the simplest LDA functionals, so I'm su= re it has the same definition in both programs) Gaussian: -1833.20351470 GAMESS: =A0 -1833.2034704727 I have done those calculations using the same grid, using tight convergence criteria. I've found out that Gaussian uses slightly different cc-pVDZ basi= s set than the one present in Basis Set Exchange, but using this basis set wi= th GAMESS has left the results unchanged. I have also tried different guesses, and SCF algorithms, but without success. Here are keywords used in inputs for above calculations. Gaussian: #p m05/cc-pvdz nosymm iop(6/7=3D3) scf=3Dtight GAMESS: =A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END =A0$CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTTYP=3DM05 $END =A0$SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END =A0$SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END =A0$DFT NRAD=3D75 NLEB=3D302 $END I would appreciate any kind of help. Best regards, Piotr Nowak E-mail to subscribers: CHEMISTRY]^[ccl.net or use: =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml=A0 =A0 =A0http://www.ccl.net/spammers.txt--0-46328946-1274842094=:80568 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
The most likely scenario is the basis se= t linear dependency. GAMESS remove the linear dependent (or more precisely,= the near linear dependent) component in the basis set space. This certainl= y will slightly change the energies. Here is an example output from GAMESS.= You can check your log file for similar information:
 

 NUMBER OF CARTESIAN ATOMIC ORBITALS=3D   &nbs= p;    166
 NUMBER OF SPHERICAL CONTAMINANTS DROPPED= =3D     0
 NUMBER OF LINEARLY DEPENDENT MOS DRO= PPED=3D     2
 TOTAL NUMBER OF MOS IN VARIATION= SPACE=3D     164
 THE INPUT BASIS SET CONTAINS APPROXIMATE LINEAR DEPENDENCE.
&= nbsp;THE SMALLEST EIGENVALUE OF THE OVERLAP MATRIX IS   2.898259E= -09
 THERE ARE    2 EIGENVALUES LESS THAN QMTT= OL=3D  1.00E-07
 EIGENVECTORS BELOW -QMTTOL- ARE DROPPE= D FROM THE MO SPACE,
 IN ORDER TO ELIMINATE THE APPROXIMATE LINEAR = DEPENDENCE.
 THIS WILL MOST LIKELY CHANGE THE ENERGY ON THE ORDER OF TENS OF = MICROHARTREES,
 DEPENDING ON THE NUMBER OF ORBITALS REMOVED.  = THE VALUE OF QMTTOL CAN BE
 CHANGED IN $CONTRL: JOBS WITH EIGENVALU= ES BELOW 1.0E-07 PROBABLY WON'T
 CONVERGE.  EIGENVALUES BETWEE= N 1.0E-07 AND 1.0E-06 MAY REQUIRE LOOSENING OF
 THE DENSITY CRITERI= ON (CONV IN $SCF), MORE ACCURATE INTEGRAL EVALUATION
 (ICUT=3D11 IN= $CONTRL), MORE ACCURATE DIRECT SCF FOCK MATRIX
 CONSTRUCTION (FDIF= F=3D.FALSE. IN $SCF), OR CHANGING THE SCF CONVERGER
 (DIIS=3D.TRUE.= IN $SCF).
 
Hope this solves the mystery.
 
Jiabo

--- On Tue, 5/25/10, Gustavo Mercier gamercier+/-yahoo= .com <owner-chemistry^^^ccl.net> wrote:

From: Gustavo Mercier gamercier+/-yahoo.com <o= wner-chemistry^^^ccl.net>
Subject: CCL:G: Different single-point DFT en= ergy between GAMESS and Gaussian
To: "Li, Jiabo " <jiaboli^^^ya= hoo.com>
Date: Tuesday, May 25, 2010, 3:32 PM

Hi!

In addition to the many suggestions that you have rece= ived I would add:

1. GAMESS direct scf has several short cuts. Look = at the control keyword group for this. I would get rid of it for both progr= ams.
2. DIIS also has adjustable parameters, including how much 'history= ' you keep.
3. With large basis sets there may be some linear dependenci= es and the programs may automatically make changes in the basis set. Check = your output.

Review the GAMESS documentation and check out the fine = print. Look at the file "refs.pdf", for example. The developers have made a= variety of choices in the implementation of different algorithms and they = may tell you that their choices may result in small differences. However, t= hese can easily be in the millihartree or less. You may conclude that getti= ng the exactly the same result is not reasonable. This does not even include such details as compiler flags and optimization schemes used with = different compilers.
 

--
Gustavo A. Mercier, Jr., MD, PhD
gamercier|*|= yahoo.com
Gustavo.Mercier|*|bmc.org
gumercie|*|bu.edu
617-414-6440=



From: Piotr Nowak piotrnowa= k[*]student.uw.edu.pl <owner-chemistry|*|ccl.net>
To: "Mercier, Gustavo, " <gamercier|*|= yahoo.com>
Sent: Tue,= May 25, 2010 1:53:20 PM
Subject: CCL:G: Different single-point DFT energy between GAMESS and Gauss= ian

First of all, thanks everyone for response. Some questions and suggest= ions appeared; I'll try to answer them briefly:

-I've been using exactly the same structures for the single point ener= gy calculations;
-I have been using spherical harmonics in both programs. Gaussian uses= them by default, and I have ensured their use in GAMESS with "ISPHER=3D+1"= keyword. The number of cartesian basis fuinctions is the same;
-Gaussian manual states that default grid uses 75 radial shells and 30= 2 angular points/shell. I have been using the same grid in GAMESS thanks to= "NRAD=3D75" and  "NLEB=3D302" keywords. I also suspected that grid ha= ndling might be implemented differently in both programs, therefore I tried= some "super-ultra-extra-fine" grid with 250 radial shells and 974 angular = points/shell (using "Int(Grid=3D250974)" keyword in Gaussian). Unluckily, t= he energy difference remained within the same order of magnitude as it was = with former grid;
-The relative energies are still different. If you compare e.g. differ= ent geometries of the same molecule, or activation energies, the error is s= till 10^(-4) hartree.

I would agree with Soren - there must be some "hidden" adjustable para= meters, but I have no idea which one can cause these differences. I still h= ope it is possible to get the same results using both programs. 

Kind regards,
Piotr


On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piot= rnowak!^!student.uw.edu.pl <owner-chemistry= ]^[ccl.net> wrote:

Sent to CCL by: "P= iotr  Nowak" [piotrnowak~!~student.uw.edu.pl]
Dear CCL users,
I'm trying to reproduce single point energy obtained with Gaussian 03 usi= ng
GAMESS US. Hartree-Fock energy is almost exactly the same e.g.
Gau= ssian: -1849.26414782
GAMESS:   -1849.2641478646

Unfortunate= ly my attempts to get the same results using DFT failed. The
energy diff= erences between both programs are unreasonably huge. Here are some
examp= les of results for different functionals (the same case as above-
mentio= ned HF example):
M05-2X
Gaussian: -1855.79754118
GAMESS:   -1= 855.7976587495
SVWN5
Gaussian: -1845.45112047
GAMESS:   -1845= .4510666810
Slater (also known as Dirac, one of the simplest LDA functio= nals, so I'm sure
it has the same definition in both programs)
Gaussian: -= 1833.20351470
GAMESS:   -1833.2034704727

I have done those c= alculations using the same grid, using tight convergence
criteria. I've = found out that Gaussian uses slightly different cc-pVDZ basis
set than t= he one present in Basis Set Exchange, but using this basis set with
GAME= SS has left the results unchanged. I have also tried different guesses,
= and SCF algorithms, but without success.

Here are keywords used in i= nputs for above calculations.
Gaussian:
#p m05/cc-pvdz nosymm iop(6/7= =3D3) scf=3Dtight

GAMESS:
 $BASIS EXTFIL=3D.TRUE. GBASIS=3DC= CPVDZGN $END
 $CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTT= YP=3DM05 $END
 $SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END
 $= SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END
 $DFT NRAD=3D75 NLEB=3D302 $= END

I would appreciate any kind of help.
Best regards,
Piotr Nowak




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--0-46328946-1274842094=:80568-- From owner-chemistry@ccl.net Wed May 26 02:57:00 2010 From: "Soren Eustis soren.eustis:_:env.ethz.ch" To: CCL Subject: CCL: NBO and NTO Visualization Message-Id: <-41968-100526025233-28870-mJ7d7p2hgKOU2TRtdSQEOg/a\server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3357708722_13318297" Date: Wed, 26 May 2010 08:52:00 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soren.eustis+*+env.ethz.ch] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3357708722_13318297 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Can anyone tell me exactly how to handle the output from an NBO or NTO calculation? I am specifically looking to visualize the NBO from a .fchk file in GV5 or possible chemcraft.. Am I trying to visualize the density o= f all occupied orbitals? For the NTO, which orbital or density do I pick to visualize in order to se= e the =8Cparticle=B9 or the =8Chole=B9 as referenced in Miller, JCP, 118 (2003)? I have found a few good sites on NBO visualization, but none on NTO. The fact is that they are starting of at a point past where my knowledge begins= ! If anyone has the time and patience to walk me through this =AD I would be appreciative. It feels a bit like when I was learning C++ and very few people I asked for advice remembered what it was like to know nothing about C++. Thus, their advice sounded like something from a Klingon text. =20 --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren/./env.ethz.ch --B_3357708722_13318297 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable NBO and NTO Visualization Can anyone tell me exactly how to handle the output from an NBO or NTO cal= culation?  I am specifically looking to visualize the NBO from a .fchk = file in GV5 or possible chemcraft..  Am I trying to visualize the densi= ty of all occupied orbitals?  

For the NTO, which orbital or density do I pick to visualize in order to se= e the ‘particle’ or the ‘hole’ as referenced in Mill= er, JCP, 118 (2003)?  

I have found a few good sites on NBO visualization, but none on NTO.  = The fact is that they are starting of at a point past where my knowledge beg= ins!  

If anyone has the time and patience to walk me through this – I would= be appreciative.  It feels a bit like when I was learning C++ and very= few people I asked for advice remembered what it was like to know nothing a= bout C++.  Thus, their advice sounded like something from a Klingon tex= t.
 
--
Dr. Soren N. Eustis
ETH – Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren/./env.ethz.ch
 --B_3357708722_13318297-- From owner-chemistry@ccl.net Wed May 26 04:55:00 2010 From: "Sayed El-Mes elsayed.elmes#%#yahoo.com" To: CCL Subject: CCL: High and low spin of dinuclear complexes Message-Id: <-41969-100526045258-32697-U3MnvKgIE5kfDo/sgxV0zQ:_:server.ccl.net> X-Original-From: "Sayed El-Mes" Date: Wed, 26 May 2010 04:52:56 -0400 Sent to CCL by: "Sayed El-Mes" [elsayed.elmes::yahoo.com] Dear All, I want to optimize the structures of the high spin and low spin of complexes like this one: [(NH3)4-Co-O-Co-(NH3)4]2+, where oxo is a bridge between two cobalt cations (II). The total spin of this complex is 1. How can specify the multiplicity in the input file in case of high and low spin of this complexes. Thanks, Sayed From owner-chemistry@ccl.net Wed May 26 06:08:00 2010 From: "Gerald Knizia knizia[#]theochem.uni-stuttgart.de" To: CCL Subject: CCL: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41970-100526060601-8961-ev2HMXo8REvZ2fFoe0GeTw-,-server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 May 2010 12:05:52 +0200 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia.[*].theochem.uni-stuttgart.de] On Wednesday 26 May 2010 00:32, Gustavo Mercier gamercier+/-yahoo.com wrote: > 1. GAMESS direct scf has several short cuts. Look at the control keyword > group for this. I would get rid of it for both programs. Direct SCF is not supposed to cause noticeable changes in the resulting energy, and certainly not for a SCF method (where the energy error depends only in second order on the error of the orbitals). > 2. DIIS also has adjustable parameters, including how much 'history' > you keep. This impacts only how fast you reach the solution, and in rare unfortunate cases also which solution you reach (e.g., convergence on a different minimum etc). It does not affect the final energy for equivalent solutions. > 3. With large basis sets there may be some linear dependencies and the > programs may automatically make changes in the basis set. Check your > output. cc-pVDZ is not a large basis set. Getting singular overlap matrices with this set is pretty much impossible. Another thing which actually can cause such discrepancies occurs in open-shell systems (namely, the choice of open-shell treatment: restricted open shell vs unrestricted open shell vs multi-reference open-shell.). Some programs might default to restricted HF treatments but unrestricted KS treatments (because spin is a two-particle quantity, and as such is not well-defined in KS anyway). Not even the DF/RI approximation is a good candidate, because this approximation leads to negligible errors in relative energies when using decent auxiliary basis sets (e.g., the Weigend ones). Different programs really *ARE* supposed to give the same energies for the same systems. This is one of the things that generally worked very well in quantum chemistry. -- Gerald Knizia From owner-chemistry@ccl.net Wed May 26 08:39:00 2010 From: "Thomas Gkourmpis thomas.gkourmpis,+,borealisgroup.com" To: CCL Subject: CCL:G: Reaction Rate Software Message-Id: <-41971-100526083717-23633-zAdjEACBTo0V+PcSlIc/vw(a)server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Wed, 26 May 2010 08:37:14 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis:-:borealisgroup.com] Hello Can anybody suggest a user freindly program that can caclulate reaction rates from files (products, reactants and TS)that have been obtained from Gaussian? thanks a lot in advance Thomas Gkourmpis From owner-chemistry@ccl.net Wed May 26 09:13:00 2010 From: "sana zafar zafsana**gmail.com" To: CCL Subject: CCL:G: Getting Largest value of alpha coefficient Message-Id: <-41972-100526020711-26542-lS/MqfskGzDDDzuUgUWZjw^server.ccl.net> X-Original-From: "sana zafar" Date: Wed, 26 May 2010 02:07:09 -0400 Sent to CCL by: "sana zafar" [zafsana]-[gmail.com] Dear Member I am using Gaussian 03 .I am getting a warning while calculating freq cal with HF/631G basis set. **** Warning!!: The largest alpha MO coefficient is 0.12489518D+02 Please resolve my problem. From owner-chemistry@ccl.net Wed May 26 09:48:00 2010 From: "Jovan Jose jovanjose^-^gmail.com" To: CCL Subject: CCL: calculating ESP fitted chrages using GMESS Message-Id: <-41973-100526063112-10824-N+L5B/xwtZYyb9E0zwVpxg===server.ccl.net> X-Original-From: Jovan Jose Content-Type: multipart/alternative; boundary=0015174a0ef4528e5704877cc572 Date: Wed, 26 May 2010 12:31:03 +0200 MIME-Version: 1.0 Sent to CCL by: Jovan Jose [jovanjose*|*gmail.com] --0015174a0ef4528e5704877cc572 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Everyone, Is there a wayout to clauclate the ESP(Elctrostatic potential) fitted charges uisng GAMESS ? Or are there some freewares by which i can calculate the same? Thanks in advance for the reply Best regards Jovan Jose --=20 Jovan Jose Lehrstuhl f=FCr Theoretische Chemie Ruhr-Universit=E4t Bochum D-44780 Bochum Germany Telephone: ++49 (0)234 32 28568 e-mail: jovan.jose]~[theochem.ruhr-uni-bochum.de --0015174a0ef4528e5704877cc572 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Everyone,

Is=A0 there a wayout to clauclate the E= SP(Elctrostatic potential) fitted charges uisng GAMESS ? Or are there some = freewares by which i can calculate the same?

Thanks in advance for t= he reply
Best regards
Jovan Jose


--
Jovan Jose
Lehrstuhl f=FCr = Theoretische Chemie
Ruhr-Universit=E4t Bochum
D-44780 Bochum =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
Germany
Telephone: ++49 (0)234 32 2= 8568
e-mail: j= ovan.jose]~[theochem.ruhr-uni-bochum.de


--0015174a0ef4528e5704877cc572-- From owner-chemistry@ccl.net Wed May 26 10:24:00 2010 From: "med mohamed m.maatallah _ ucam.ac.ma" To: CCL Subject: CCL:G: enthalpy and entropy value Message-Id: <-41974-100526053808-21098-eDAy5arUVRUdMo0s1jdFiw ~~ server.ccl.net> X-Original-From: "med mohamed" Date: Wed, 26 May 2010 05:38:07 -0400 Sent to CCL by: "med mohamed" [m.maatallah__ucam.ac.ma] Dear colleagues, I would like to know how I can determine the value of the enthalpy and the entropy from a file out obtained from a DFT calculation on gaussian? From owner-chemistry@ccl.net Wed May 26 10:58:00 2010 From: "Deskins, N Aaron nadeskins-$-WPI.EDU" To: CCL Subject: CCL: Creating surfaces from crystal structures Message-Id: <-41975-100526090112-26704-vfgBFYMtKZa1tbBrWP/VKw!=!server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 09:00:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins a WPI.EDU] Thank you for the responses. GDIS looks like it has real potential. Aaron -----Original Message----- Subject: CCL: Creating surfaces from crystal structures Sent to CCL by: "Nathaniel Aaron Deskins" [nadeskins##wpi.edu] I'm looking for software that will create a surface (i.e. 111 or 110 or wh= atever) from a given bulk crystal structure (from a cif file or some other = format). I'd really like the software to create a surface cell that I can u= se for some periodic simulations.=20 =20 From owner-chemistry@ccl.net Wed May 26 11:42:00 2010 From: "Fabio Molfetta fabioamsc . ig.com.br" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41976-100526100649-20455-22G/Rq5f0xbq5PJ/13cigw^-^server.ccl.net> X-Original-From: "Fabio Molfetta" Date: Wed, 26 May 2010 10:06:47 -0400 Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] Are there 3D structure generator programs free of charge to virtual screening? I kwown that Corina and Omega but these programs are not free. From owner-chemistry@ccl.net Wed May 26 12:18:00 2010 From: "Andreini Matteo mandreini_-_sienabiotech.it" To: CCL Subject: CCL: Library enumeration software Message-Id: <-41977-100526100708-20800-vDpx8FKaL3zOS5txcu0HxQ---server.ccl.net> X-Original-From: Andreini Matteo Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 16:06:55 +0200 MIME-Version: 1.0 Sent to CCL by: Andreini Matteo [mandreini|sienabiotech.it] Hi Dick, I suggest you "Reactor" from chemaxon (http://www.chemaxon.com/products/re= actor/#1). It is a commercial software but it should be free for academics = (check I'm not sure). However contact chemaxon and check if it fit your nee= ds. Enjoy Matteo Andreini ------------------------------------------------------------- Matteo Andreini Drug Design Siena Biotech S.p.A. Strada del Petriccio e Belriguardo, 35 53100 Siena - = ITALY Tel :(+39) 0577 381 415 Fax :(+39) 0577 381 410 mandreini!A!sienabiotec= h.it http://www.sienabiotech.it/ -----Original Message----- > From: owner-chemistry+mandreini=3D=3Dsienabiotech.it!A!ccl.net [mailto:owner-= chemistry+mandreini=3D=3Dsienabiotech.it!A!ccl.net] On Behalf Of Richard Harp= er drrwharper!^!gmail.com Sent: Tuesday, May 18, 2010 10:48 PM To: Andreini Matteo Subject: CCL: Library enumeration software Sent to CCL by: Richard Harper [drrwharper^^^gmail.com] What software are you using to enumerate (virtual or real) libraries of chemicals from a scaffold and sets of reagents? Among the requirements are the ability to enumerate large libraries (10^6 or more compounds); some flexibility in naming (ability to record the identifiers of the reactants); and Open Source or free academic license (or very inexpensive). Any suggestions are appreciated. Dick Harper Indiana University-Purdue University Indianapolis (IUPUI) -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt---------------------------------------------- This email and any files transmitted with it are confidential and intended = solely for the use of the individual or entity to whom they are addressed. = If you have received this email in error please notify the system manager. = This message contains confidential information and is intended only for the= individual named. If you are not the named addressee you should not dissem= inate, distribute or copy this e-mail. Please notify the sender immediately= by e-mail if you have received this e-mail by mistake and delete this e-ma= il from your system. If you are not the intended recipient you are notified= that disclosing, copying, distributing or taking any action in reliance on= the contents of this information is strictly prohibited. From owner-chemistry@ccl.net Wed May 26 12:53:00 2010 From: "Piotr Nowak piotrnowak*o*student.uw.edu.pl" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41978-100526105424-14984-dy/YMzUo1WZFWld2orMTWA,,server.ccl.net> X-Original-From: Piotr Nowak Content-Type: multipart/alternative; boundary=0015174c10bc70d7a80487807270 Date: Wed, 26 May 2010 16:54:12 +0200 MIME-Version: 1.0 Sent to CCL by: Piotr Nowak [piotrnowak||student.uw.edu.pl] --0015174c10bc70d7a80487807270 Content-Type: text/plain; charset=ISO-8859-1 Several new plausible solutions to the problems have been made. Because the problem has been more difficult than I had thought, I've checked those suggestions on a simpler test case, namely: 1-fluoroethanol, using the geometry below: C 6 -1.371551 -0.189402 -0.078069 C 6 0.055735 -0.002315 0.345325 H 1 -1.765264 -1.132234 0.321003 H 1 -1.422818 -0.219081 -1.174187 H 1 -1.987781 0.640525 0.287358 O 8 0.815913 -1.025112 -0.171888 H 1 0.154695 0.068673 1.446323 F 9 0.519096 1.212587 -0.140203 H 1 1.716903 -0.919975 0.152892 - Christopher Cramer suggested that different spatial orientation may cause different results. The "nosymm" Gaussian keyword indeed suppreses any orientation changes, so input orientation is used throughout the calculations. GAMESS doesn't change the orientation by default, so calculations performed using "nosymm" are made on the same geometry. I was curious if changing the initial orientation (called "InitOr in the table below - different than the orientation above) to the standard one, can change the results significantly. If "nosymm" is not present, Gaussian rotates the molecule to the standard orientation (StdOr). In order to do the same using GAMESS, "COORD=PRINAXIS" keyword is required. I've found out that when using standard orientation from the Gaussian output and pasting it to the GAMESS input (now without "coord=prinaxis), GAMESS gives different result than by rotating the molecule to the principal axis by itself! Therefore in all subsequent GAMESS calculations I was using standard orientation from Gaussian output (the one above). The results are presented below (using M05/cc-pVDZ and grid(75,302)), together with HF energies, which are pretty much reproducible, and M05 calculations using much better than standard grid (250,974): Gaussian: -254.175261128 (InitOr,nosymm) -254.175313014 (StdOr transformed from InitOr by Gaussian) GAMESS: -254.1753800399 (InitOr) -254.1753738096 (InitOr with "COORD=PRINAXIS" keyword) -254.1753375023 (StdOr) Grid(250,974): -254.175301121 (Gaussian, StdOr) -254.1753365149 (GAMESS, InitOr, "PRINAXIS") -254.1753372591 (GAMESS, StdOr) Hartree-Fock: -252.967151367 (Gaussian) -252.9671513780 (GAMESS) - Many people said that linear dependencies could be the cause. That's very unlikely with cc-pVDZ, and there are no linearly dependent MOs present in my GAMESS outputs. - The symmetry is C1 in all cases. - There are no transition metals present. - I know that GAMESS interprets CCD keyword as cc-pV(D+d)Z basis set instead of cc-pVDZ. That's why I was using explicitely defined cc-pVDZ atomic basis set in GAMESS, exactly the one used by Gaussian ("gfinput" switches on printing of basis set info in Gaussian). - Another source of error is grid pruning in Gaussian. To avoid this, grid should be requested using e.g. "int(grid=75302)" instead of "int(grid=finegrid)". There are two weighing schemes available in Gaussian. The scheme of Scuseria and Stratman ("ssweights) is the default, and Becke scheme can be requested using "bweights". I don't have any ideas how weighing is performed by GAMESS. Unfortunatly changing those options still does not give similar results: -254.175313014 (Gaussian - int(grid=finegrid), ssweights) -254.175298048 (Gaussian - int(grid=75302), ssweights) -254.175297910 (Gaussian - int(grid=75302), bweights) -254.1753375023 (GAMESS) I'm afraid hat the whole idea of reproducibility of results is going to fail in case of DFT, but I still hope that it can see the light in the darkness. Somwhere... Best Regards, Piotr On Tue, May 25, 2010 at 7:53 PM, Piotr Nowak piotrnowak[*]student.uw.edu.pl wrote: > First of all, thanks everyone for response. Some questions and suggestions > appeared; I'll try to answer them briefly: > > -I've been using exactly the same structures for the single point energy > calculations; > -I have been using spherical harmonics in both programs. Gaussian uses them > by default, and I have ensured their use in GAMESS with "ISPHER=+1" keyword. > The number of cartesian basis fuinctions is the same; > -Gaussian manual states that default grid uses 75 radial shells and 302 > angular points/shell. I have been using the same grid in GAMESS thanks to > "NRAD=75" and "NLEB=302" keywords. I also suspected that grid handling > might be implemented differently in both programs, therefore I tried some > "super-ultra-extra-fine" grid with 250 radial shells and 974 angular > points/shell (using "Int(Grid=250974)" keyword in Gaussian). Unluckily, the > energy difference remained within the same order of magnitude as it was with > former grid; > -The relative energies are still different. If you compare e.g. different > geometries of the same molecule, or activation energies, the error is still > 10^(-4) hartree. > > I would agree with Soren - there must be some "hidden" adjustable > parameters, but I have no idea which one can cause these differences. I > still hope it is possible to get the same results using both programs. > > Kind regards, > Piotr > > > On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piotrnowak!^! > student.uw.edu.pl > > wrote: > >> >> Sent to CCL by: "Piotr Nowak" [piotrnowak~!~student.uw.edu.pl] >> Dear CCL users, >> >> I'm trying to reproduce single point energy obtained with Gaussian 03 >> using >> GAMESS US. Hartree-Fock energy is almost exactly the same e.g. >> Gaussian: -1849.26414782 >> GAMESS: -1849.2641478646 >> >> Unfortunately my attempts to get the same results using DFT failed. The >> energy differences between both programs are unreasonably huge. Here are >> some >> examples of results for different functionals (the same case as above- >> mentioned HF example): >> M05-2X >> Gaussian: -1855.79754118 >> GAMESS: -1855.7976587495 >> SVWN5 >> Gaussian: -1845.45112047 >> GAMESS: -1845.4510666810 >> Slater (also known as Dirac, one of the simplest LDA functionals, so I'm >> sure >> it has the same definition in both programs) >> Gaussian: -1833.20351470 >> GAMESS: -1833.2034704727 >> >> I have done those calculations using the same grid, using tight >> convergence >> criteria. I've found out that Gaussian uses slightly different cc-pVDZ >> basis >> set than the one present in Basis Set Exchange, but using this basis set >> with >> GAMESS has left the results unchanged. I have also tried different >> guesses, >> and SCF algorithms, but without success. >> >> Here are keywords used in inputs for above calculations. >> Gaussian: >> #p m05/cc-pvdz nosymm iop(6/7=3) scf=tight >> >> GAMESS: >> $BASIS EXTFIL=.TRUE. GBASIS=CCPVDZGN $END >> $CONTRL ISPHER=+1 SCFTYP=RHF RUNTYP=ENERGY DFTTYP=M05 $END >> $SYSTEM PARALL=.TRUE. MWORDS=200 $END >> $SCF DIRSCF=.TRUE. DIIS=.TRUE. $END >> $DFT NRAD=75 NLEB=302 $END >> >> I would appreciate any kind of help. >> Best regards, >> Piotr Nowak>> E-mail to subscribers: CHEMISTRY]^[ccl.net or >> use:>> >> E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.netor use>> >> >> > > -- http://www.slayer.net/us/orderwpb --0015174c10bc70d7a80487807270 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Several new plausible solutions to the problems have been made. Becaus= e the problem has been more difficult than I had thought, I've checked = those suggestions on a simpler test case, namely: 1-fluoroethanol, using th= e geometry below:

=A0=A0 =A0C =A06 =A0 =A0-1.371551 =A0 -0.189402 =A0 -0.= 078069
=A0=A0 =A0C =A06 =A0 =A0 0.055735 =A0 -0.002315 =A0 =A00.3= 45325
=A0=A0 =A0H =A01 =A0 =A0-1.765264 =A0 -1.132234 =A0 =A00.32= 1003
=A0=A0 =A0H =A01 =A0 =A0-1.422818 =A0 -0.219081 =A0 -1.17418= 7
=A0=A0 =A0H =A01 =A0 =A0-1.987781 =A0 =A00.640525 =A0 =A00.287358
=A0=A0 =A0O =A08 =A0 =A0 0.815913 =A0 -1.025112 =A0 -0.171888
=A0=A0 =A0H =A01 =A0 =A0 0.154695 =A0 =A00.068673 =A0 =A01.446323
<= div>=A0=A0 =A0F =A09 =A0 =A0 0.519096 =A0 =A01.212587 =A0 -0.140203
=A0=A0 =A0H =A01 =A0 =A0 1.716903 =A0 -0.919975 =A0 =A00.152892
<= div>
- Christopher Cramer suggested that different spatial or= ientation may cause different results. The "nosymm" Gaussian keyw= ord indeed suppreses any orientation changes, so input orientation is used = throughout the calculations. GAMESS doesn't change the orientation by d= efault, so calculations performed using "nosymm" are made on the = same geometry. I was curious if changing the initial orientation (called &q= uot;InitOr in the table below - different than the orientation above) to th= e standard one, can change the results significantly. If "nosymm"= is not present, Gaussian rotates the molecule to the standard orientation = (StdOr). In order to do the same using GAMESS, "COORD=3DPRINAXIS"= keyword is required. I've found out that when using standard orientati= on from the Gaussian output and pasting it to the GAMESS input (now without= "coord=3Dprinaxis), GAMESS gives different result than by rotating th= e molecule to the principal axis by itself! Therefore in all subsequent GAM= ESS calculations I was using standard orientation from Gaussian output (the= one above). The results are presented below (using M05/cc-pVDZ and grid(75= ,302)), together with HF energies, which are pretty much reproducible, and = M05 calculations using much better than standard grid (250,974):

Gaussian:
-254.175261128 =A0(InitOr,nosymm)
-254.175313014 =A0(StdOr transformed from InitOr by Gaussian)
GAMESS:
-254.1753800399 (InitOr)
-254.1753738096 = (InitOr with "COORD=3DPRINAXIS" keyword)
-254.1753375023 (StdOr)
Grid(250,974):
-254.175301= 121 =A0(Gaussian, StdOr)
-254.1753365149 (GAMESS, InitOr, "P= RINAXIS")
-254.1753372591 (GAMESS, StdOr)
Hartree-= Fock:
-252.967151367 =A0(Gaussian)
-252.9671513780 (GAMESS)
<= div>=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0
- Many people said = that linear dependencies could be the cause. That's very unlikely with = cc-pVDZ, and there are no linearly dependent MOs present in my GAMESS outpu= ts.=A0
- The symmetry is C1 in all cases.
- There are no transition= metals present.=A0
- I know that GAMESS interprets CCD keyword a= s cc-pV(D+d)Z basis set instead of cc-pVDZ. That's why I was using expl= icitely defined cc-pVDZ atomic basis set in GAMESS, exactly the one used by= Gaussian ("gfinput" switches on printing of basis set info in Ga= ussian).
- Another source of error is grid pruning in Gaussian. To avoid this, = grid should be requested using e.g. "int(grid=3D75302)" instead o= f "int(grid=3Dfinegrid)". There are two weighing schemes availabl= e in Gaussian. The scheme of Scuseria and Stratman ("ssweights) is the= default, and Becke scheme can be requested using "bweights". I d= on't have any ideas how weighing is performed by GAMESS. Unfortunatly c= hanging those options still does not give similar results:
-254.175313014 =A0(Gaussian - int(grid=3Dfinegrid), ssweights)
-254.175298048 =A0(Gaussian - int(grid=3D75302), ssweights)
-2= 54.175297910 =A0(Gaussian - int(grid=3D75302), bweights)
-254.175= 3375023 (GAMESS)

I'm afraid hat the whole idea of reproducibility of= results is going to fail in case of DFT, but I still hope that it can see = the light in the darkness. Somwhere...

Best Regard= s,
Piotr=A0

On Tue, May 25, 2010 at 7= :53 PM, Piotr Nowak piotrnowak[*]stude= nt.uw.edu.pl <owner-chemistry:+:ccl.net> wrote:
First of all, thanks everyone for resp= onse. Some questions and suggestions appeared; I'll try to answer them = briefly:

-I've been using exactly the same structures for th= e single point energy calculations;
-I have been using spherical harmonics in both programs. Gaussian uses= them by default, and I have ensured their use in GAMESS with "ISPHER= =3D+1" keyword. The number of cartesian basis fuinctions is the same;<= /div>
-Gaussian manual states that default grid uses 75 radial shells and 30= 2 angular points/shell. I have been using the same grid in GAMESS thanks to= "NRAD=3D75" and =A0"NLEB=3D302" keywords. I also suspe= cted that grid handling might be implemented differently in both programs, = therefore I tried some "super-ultra-extra-fine" grid with 250 rad= ial shells and 974 angular points/shell (using "Int(Grid=3D250974)&quo= t; keyword in Gaussian). Unluckily, the energy difference remained within t= he same order of magnitude as it was with former grid;
-The relative energies are still different. If you compare e.g. differ= ent geometries of the same molecule, or activation energies, the error is s= till 10^(-4) hartree.

I would agree with Soren - t= here must be some "hidden" adjustable parameters, but I have no i= dea which one can cause these differences. I still hope it is possible to g= et the same results using both programs.=A0

Kind regards,
Piotr


On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piotrnowak!^!student.uw.edu.pl <owner-chemistry]^[ccl.net> wrote:

Sent to CCL by: "Piotr =A0Nowak" [piotrnowak~!~student.uw.edu.pl]
Dear CCL users,

I'm trying to reproduce single point energy obtained with Gaussian 03 u= sing
GAMESS US. Hartree-Fock energy is almost exactly the same e.g.
Gaussian: -1849.26414782
GAMESS: =A0 -1849.2641478646

Unfortunately my attempts to get the same results using DFT failed. The
energy differences between both programs are unreasonably huge. Here are so= me
examples of results for different functionals (the same case as above-
mentioned HF example):
M05-2X
Gaussian: -1855.79754118
GAMESS: =A0 -1855.7976587495
SVWN5
Gaussian: -1845.45112047
GAMESS: =A0 -1845.4510666810
Slater (also known as Dirac, one of the simplest LDA functionals, so I'= m sure
it has the same definition in both programs)
Gaussian: -1833.20351470
GAMESS: =A0 -1833.2034704727

I have done those calculations using the same grid, using tight convergence=
criteria. I've found out that Gaussian uses slightly different cc-pVDZ = basis
set than the one present in Basis Set Exchange, but using this basis set wi= th
GAMESS has left the results unchanged. I have also tried different guesses,=
and SCF algorithms, but without success.

Here are keywords used in inputs for above calculations.
Gaussian:
#p m05/cc-pvdz nosymm iop(6/7=3D3) scf=3Dtight

GAMESS:
=A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END
=A0$CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTTYP=3DM05 $END
=A0$SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END
=A0$SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END
=A0$DFT NRAD=3D75 NLEB=3D302 $END

I would appreciate any kind of help.
Best regards,
Piotr Nowak



-=3D This is automatically added to each message by the mailing script =3D-
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--0015174c10bc70d7a80487807270-- From owner-chemistry@ccl.net Wed May 26 13:28:01 2010 From: "Jon Fuller fbsjf=leeds.ac.uk" To: CCL Subject: CCL: calculating ESP fitted chrages using GMESS Message-Id: <-41979-100526111953-16121-jaRMt2Lxnfm0DFxJjsoppQ^server.ccl.net> X-Original-From: Jon Fuller Content-Type: multipart/alternative; boundary=000325557e1e8596dd048780cdb7 Date: Wed, 26 May 2010 16:19:40 +0100 MIME-Version: 1.0 Sent to CCL by: Jon Fuller [fbsjf-#-leeds.ac.uk] --000325557e1e8596dd048780cdb7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jovan, You might consider the RED tools suite. http://q4md-forcefieldtools.biz/RED/ Jon On 26 May 2010 11:31, Jovan Jose jovanjose^-^gmail.com < owner-chemistry_-_ccl.net> wrote: > Dear Everyone, > > Is there a wayout to clauclate the ESP(Elctrostatic potential) fitted > charges uisng GAMESS ? Or are there some freewares by which i can calcula= te > the same? > > Thanks in advance for the reply > Best regards > Jovan Jose > > > -- > Jovan Jose > Lehrstuhl f=FCr Theoretische Chemie > Ruhr-Universit=E4t Bochum > D-44780 Bochum > Germany > Telephone: ++49 (0)234 32 28568 > e-mail: jovan.jose[]theochem.ruhr-uni-bochum.de > > > --000325557e1e8596dd048780cdb7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jovan,

You might consider the RED tools suite.

Jon

On 26 May 2010 11:31, Jovan Jose jovanjose^-^g= mail.com <owner-chemistry_-_ccl.net> wrote:
Dear Everyone,

Is=A0 there a wayout to clauclate the E= SP(Elctrostatic potential) fitted charges uisng GAMESS ? Or are there some = freewares by which i can calculate the same?

Thanks in advance for t= he reply
Best regards
Jovan Jose


--
Jovan = Jose
Lehrstuhl f=FCr Theoretische Chemie
Ruhr-Universit=E4t BochumD-44780 Bochum =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
Germany
Tel= ephone: ++49 (0)234 32 28568
e-mail: jovan.jose[]theochem.ruhr-uni-bochum.de



--000325557e1e8596dd048780cdb7-- From owner-chemistry@ccl.net Wed May 26 14:01:01 2010 From: "Jamin Krinsky jamink+*+berkeley.edu" To: CCL Subject: CCL:G: Getting Largest value of alpha coefficient Message-Id: <-41980-100526120404-6635-uj/8LOjrRkRRvkHZCbog7A : server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 May 2010 09:03:40 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]|[berkeley.edu] Dear Sana, You will generally get that warning when using large basis sets. Anything on the order of 10^2 is fine to ignore as far as I've ever heard. If you see something really large like 10^5 then you want to worry. Regards, Jamin On Tue, May 25, 2010 at 11:07 PM, sana zafar zafsana**gmail.com wrote: > > Sent to CCL by: "sana =A0zafar" [zafsana]-[gmail.com] > Dear Member I am using Gaussian 03 .I am getting a warning while calculat= ing > freq cal with HF/631G basis set. > =A0**** Warning!!: The largest alpha MO coefficient is =A00.12489518D+02 > Please resolve my problem. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink a berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Wed May 26 14:37:01 2010 From: "Jeff Woodford jwoodfor|eou.edu" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41981-100526120557-8734-RyhGKDb5O7QGC/0mkpNvdw . server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 May 2010 09:05:58 -0700 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor(!)eou.edu] Something I just noticed: =A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END What is the "CCPVDZGN" basis set and how is it different than the = internally stored cc-pVDZ basis set in GAMESS or Gaussian 03? I think that is the source of your difficulty right there. -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry+jwoodfor=3D=3Deou.edu ~ ccl.net [mailto:owner-chemistry+jwoodfor=3D=3Deou.edu ~ ccl.net] On Behalf Of = Gerald Knizia knizia[#]theochem.uni-stuttgart.de Sent: Wednesday, May 26, 2010 3:06 AM To: Woodford, Jeffrey N Subject: CCL: Different single-point DFT energy between GAMESS and = Gaussian Sent to CCL by: Gerald Knizia [knizia. ~ .theochem.uni-stuttgart.de] On Wednesday 26 May 2010 00:32, Gustavo Mercier gamercier+/-yahoo.com = wrote: > 1. GAMESS direct scf has several short cuts. Look at the control = keyword > group for this. I would get rid of it for both programs. Direct SCF is not supposed to cause noticeable changes in the resulting=20 energy, and certainly not for a SCF method (where the energy error = depends=20 only in second order on the error of the orbitals). > 2. DIIS also has adjustable parameters, including how much 'history' > you keep.=20 This impacts only how fast you reach the solution, and in rare = unfortunate=20 cases also which solution you reach (e.g., convergence on a different minimum=20 etc). It does not affect the final energy for equivalent solutions. > 3. With large basis sets there may be some linear dependencies and the > programs may automatically make changes in the basis set. Check your > output.=20 cc-pVDZ is not a large basis set. Getting singular overlap matrices with this=20 set is pretty much impossible. Another thing which actually can cause such discrepancies occurs in open-shell=20 systems (namely, the choice of open-shell treatment: restricted open = shell vs=20 unrestricted open shell vs multi-reference open-shell.). Some programs = might default to restricted HF treatments but unrestricted KS treatments = (because=20 spin is a two-particle quantity, and as such is not well-defined in KS=20 anyway). Not even the DF/RI approximation is a good candidate, because this=20 approximation leads to negligible errors in relative energies when using = decent auxiliary basis sets (e.g., the Weigend ones). Different programs really *ARE* supposed to give the same energies for = the=20 same systems. This is one of the things that generally worked very well = in=20 quantum chemistry. --=20 Gerald Knizia -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 26 15:12:00 2010 From: "Heath Watts hdw115_-_psu.edu" To: CCL Subject: CCL:G: enthalpy and entropy value Message-Id: <-41982-100526115525-29209-BZ3ZruyQLjACxJ1vDIoyRw],[server.ccl.net> X-Original-From: Heath Watts Content-Type: multipart/alternative; boundary=000e0cd1b3e6a638550487814c06 Date: Wed, 26 May 2010 11:55:13 -0400 MIME-Version: 1.0 Sent to CCL by: Heath Watts [hdw115#%#psu.edu] --000e0cd1b3e6a638550487814c06 Content-Type: text/plain; charset=ISO-8859-1 First, do a frequency calculation on your geometry optimized structure; Gaussian will provide an output like this in your log or out file: Sum of electronic and thermal Enthalpies= -1416.616578 Sum of electronic and thermal Free Energies= -1416.710410 You can find these results from your terminal by typing: grep 'Sum of electronic' filename.extension These thermodynamic results are in Hartrees/particle, and are the delta-H or delta-G of formation of the respective model. Obtain the enthalpy results > from your product and reactant calculations and determine the enthalpy of the reaction: deltaH(rxn) = deltaH(products) - deltaH(reactants) Do the same for the Gibbs free energy (last line of above output labeled "Sum of electronic and thermal Free Energies"): deltaG(rxn) = deltaG(products) - deltaG(reactants) Then, use this equation to find delta-S of the reaction: deltaG(rxn) = deltaH(rxn) - T*deltaS(rxn) where T is the temperature at which you performed your frequency calculation--usually 298.15K. On Wed, May 26, 2010 at 5:38 AM, med mohamed m.maatallah _ ucam.ac.ma < owner-chemistry[]ccl.net> wrote: > > Sent to CCL by: "med mohamed" [m.maatallah__ucam.ac.ma] > Dear colleagues, I would like to know how I can determine the value of the > enthalpy and the entropy from a file out obtained from a DFT calculation on > gaussian?> > > --000e0cd1b3e6a638550487814c06 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable First, do a frequency calculation on your geometry optimized structure; Gau= ssian will provide an output like this in your log or out file:

Sum of electronic and thermal Enthalpies=3D= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -1416.616578
Sum of electronic and thermal Free Energies=3D=A0=A0=A0=A0=A0 -1416.710410<= br>
You can find these results from your terminal by typing:
grep 'Sum of electronic' filename.extension

These thermody= namic results are in Hartrees/particle, and are the delta-H or delta-G of f= ormation of the respective model. Obtain the enthalpy results from your pro= duct and reactant calculations and determine the enthalpy of the reaction:<= br>
deltaH(rxn) =3D deltaH(products) - deltaH(reactants)

Do the same= for the Gibbs free energy (last line of above output labeled "Sum of = electronic and thermal Free Energies"):

deltaG(rxn) =3D deltaG(= products) - deltaG(reactants)

Then, use this equation to find delta-S of the reaction:

deltaG(= rxn) =3D deltaH(rxn) - T*deltaS(rxn)

where T is the temperature at w= hich you performed your frequency calculation--usually 298.15K.





On Wed, May 26, 2010 at 5:38 AM, med= mohamed m.maatallah _ ucam.ac.ma <owner-chemistry[]c= cl.net> wrote:

Sent to CCL by: "med =A0mohamed" [m.maatallah__ucam.ac.ma]
Dear colleagues, I would like to know how I can determine the value of the = enthalpy and the entropy from a file out obtained from a DFT calculation on= gaussian?



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[]ccl.n= et or use:
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--000e0cd1b3e6a638550487814c06-- From owner-chemistry@ccl.net Wed May 26 15:46:01 2010 From: "Sayan Mondal sayanmondal.ncbs++gmail.com" To: CCL Subject: CCL:G: enthalpy and entropy value Message-Id: <-41983-100526122119-31195-AXyajigzB5AlKtdlLxt8ig _ server.ccl.net> X-Original-From: Sayan Mondal Content-Type: multipart/alternative; boundary=001636e90bf74d747c048781a9ce Date: Wed, 26 May 2010 21:51:07 +0530 MIME-Version: 1.0 Sent to CCL by: Sayan Mondal [sayanmondal.ncbs .. gmail.com] --001636e90bf74d747c048781a9ce Content-Type: text/plain; charset=ISO-8859-1 In a Gaussian single point energy calculation output file, the "Thermochemistry" section lists all thermochemical properties calculated, e.g. Sum of electronic and zero-point Energies= ...... Sum of electronic and thermal Energies= ..... Sum of electronic and thermal Enthalpies= ..... Sum of electronic and thermal Free Energies=...... Hope it will help. On Wed, May 26, 2010 at 3:08 PM, med mohamed m.maatallah _ ucam.ac.ma < owner-chemistry[*]ccl.net> wrote: > > Sent to CCL by: "med mohamed" [m.maatallah__ucam.ac.ma] > Dear colleagues, I would like to know how I can determine the value of the > enthalpy and the entropy from a file out obtained from a DFT calculation on > gaussian?> > > -- Sayan Mondal Graduate Student Dr. Mrinalini Puranik,s Lab National Centre for Biological Sciences, TIFR Bangalore - 560065 INDIA Ph: +91-080-23666161 --001636e90bf74d747c048781a9ce Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable In a Gaussian single point energy calculation output file, the "Thermo= chemistry" section lists all thermochemical properties calculated, e.g= .

Sum of electronic and zero-point Energies=3D=A0 ......
Sum of e= lectronic and thermal Energies=3D=A0=A0=A0=A0 .....
Sum of electronic and thermal Enthalpies=3D=A0=A0 .....
Sum of electroni= c and thermal Free Energies=3D......

Hope it will help.


<= div class=3D"gmail_quote">On Wed, May 26, 2010 at 3:08 PM, med mohamed m.ma= atallah _ ucam.ac.ma &l= t;owner-chemistry[*]ccl.net>= ; wrote:

Sent to CCL by: "med =A0mohamed" [m.maatallah__ucam.ac.ma]
Dear colleagues, I would like to know how I can determine the value of the = enthalpy and the entropy from a file out obtained from a DFT calculation on= gaussian?



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[*]ccl.n= et or use:
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--
Sayan Mondal
Graduat= e Student
Dr. Mrinalini Puranik,s Lab
National Centre for Biological = Sciences, TIFR
Bangalore - 560065
INDIA
Ph: +91-080-23666161

--001636e90bf74d747c048781a9ce-- From owner-chemistry@ccl.net Wed May 26 16:23:00 2010 From: "hugo hugomartiniano^gmail.com" To: CCL Subject: CCL:G: enthalpy and entropy value Message-Id: <-41984-100526121513-25436-Qda366XXAoDy4vYlBWwkIA||server.ccl.net> X-Original-From: hugo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 May 2010 17:14:58 +0100 MIME-Version: 1.0 Sent to CCL by: hugo [hugomartiniano|gmail.com] A comprehensive explanation of the thermochemistry output of gaussian can be found here: http://www.gaussian.com/g_whitepap/thermo.htm On 05/26/2010 10:38 AM, med mohamed m.maatallah _ ucam.ac.ma wrote: > Sent to CCL by: "med mohamed" [m.maatallah__ucam.ac.ma] > Dear colleagues, I would like to know how I can determine the value of the enthalpy and the entropy from a file out obtained from a DFT calculation on gaussian?> > > From owner-chemistry@ccl.net Wed May 26 16:57:00 2010 From: "Eduardo edulsa,+,quimica.ufpr.br" To: CCL Subject: CCL: Creating surfaces from crystal structures Message-Id: <-41985-100526125116-1057-9pM+WR8BOeLJOLKh6eneBw() server.ccl.net> X-Original-From: Eduardo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 May 2010 13:52:08 -0300 MIME-Version: 1.0 Sent to CCL by: Eduardo [edulsa]~[quimica.ufpr.br] Ladies and Gentlemen Sorry by the delay: there is another free program, xcrysden, that is capable to create cristals and surfaces. This runs under windows (using cygwin facilities), linux and other unixes (source code is provided). Cheers Eduardo On 05/26/10 10:00, Deskins, N Aaron nadeskins-$-WPI.EDU wrote: > > Sent to CCL by: "Deskins, N Aaron" [nadeskins a WPI.EDU] > Thank you for the responses. GDIS looks like it has real potential. > Aaron > > -----Original Message----- > > Subject: CCL: Creating surfaces from crystal structures > Sent to CCL by: "Nathaniel Aaron Deskins" [nadeskins##wpi.edu] > > I'm looking for software that will create a surface (i.e. 111 or 110 or whatever) from a given bulk crystal structure (from a cif file or some other format). I'd really like the software to create a surface cell that I can use for some periodic simulations. > > > > > -=his is automatically added to each message by the mailing script =-> > -- Eduardo Lemos de Sa Associated Professor at Chemistry Department Universidade Federal do Parana Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil phone: +55(41)33613300 fax : +55(41)33613186 From owner-chemistry@ccl.net Wed May 26 17:32:00 2010 From: "Vincent Leroux vincent.leroux]~[loria.fr" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41986-100526143616-28425-d13bc3mUg8HuskBwXZnnXQ!A!server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 May 2010 20:35:48 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux|a|loria.fr] Hi Fabio, You might want to read this: http://fiehnlab.ucdavis.edu/staff/kind/ChemoInformatics/Concepts/3D-conformer/ FROG code is planned to be fused into OpenBabel - and that would be nice indeed. Server here: http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog If you are from the academia you should ask for a free licence for all OpenEye software, including Omega. Regards, VL Le 26/05/10 16:06, Fabio Molfetta fabioamsc . ig.com.br a écrit : > Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] > Are there 3D structure generator programs free of charge to virtual screening? I kwown that Corina and Omega but these programs are not free.> > > From owner-chemistry@ccl.net Wed May 26 18:07:00 2010 From: "John McKelvey jmmckel-$-gmail.com" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41987-100526142139-12999-98BATifLAWO6+3brC2uz7g]_[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 May 2010 14:21:27 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel:+:gmail.com] I haven't followed all this, but I have had some accuracy problems related to convergence in both Turbomole and G03. The issue was solved in the case of Turbomole by setting thresholds such that _no_ integrals, 1e, or 2e, were omitted and in the case of G03 I used SCF=3DTIGHT. I suppose one could also consider "novarac" (sp?)in G03 also which I think eliminates a lot of grid trimming which could have an effeft on the integrals to be calculated... My wild $0.02.. John McKelvey On Wed, May 26, 2010 at 10:54 AM, Piotr Nowak piotrnowak*o*student.uw.edu.pl wrote: > Several new plausible solutions to the problems have been made. Because t= he > problem has been more difficult than I had thought, I've checked those > suggestions on a simpler test case, namely: 1-fluoroethanol, using the > geometry below: > =A0=A0 =A0C =A06 =A0 =A0-1.371551 =A0 -0.189402 =A0 -0.078069 > =A0=A0 =A0C =A06 =A0 =A0 0.055735 =A0 -0.002315 =A0 =A00.345325 > =A0=A0 =A0H =A01 =A0 =A0-1.765264 =A0 -1.132234 =A0 =A00.321003 > =A0=A0 =A0H =A01 =A0 =A0-1.422818 =A0 -0.219081 =A0 -1.174187 > =A0=A0 =A0H =A01 =A0 =A0-1.987781 =A0 =A00.640525 =A0 =A00.287358 > =A0=A0 =A0O =A08 =A0 =A0 0.815913 =A0 -1.025112 =A0 -0.171888 > =A0=A0 =A0H =A01 =A0 =A0 0.154695 =A0 =A00.068673 =A0 =A01.446323 > =A0=A0 =A0F =A09 =A0 =A0 0.519096 =A0 =A01.212587 =A0 -0.140203 > =A0=A0 =A0H =A01 =A0 =A0 1.716903 =A0 -0.919975 =A0 =A00.152892 > - Christopher Cramer suggested that different spatial orientation may cau= se > different results. The "nosymm" Gaussian keyword indeed suppreses any > orientation changes, so input orientation is used throughout the > calculations. GAMESS doesn't change the orientation by default, so > calculations performed using "nosymm" are made on the same geometry. I wa= s > curious if changing the initial orientation (called "InitOr in the table > below - different than the orientation above) to the standard one, can > change the results significantly. If "nosymm" is not present, Gaussian > rotates the molecule to the standard orientation (StdOr). In order to do = the > same using GAMESS, "COORD=3DPRINAXIS" keyword is required. I've found out= that > when using standard orientation from the Gaussian output and pasting it t= o > the GAMESS input (now without "coord=3Dprinaxis), GAMESS gives different > result than by rotating the molecule to the principal axis by itself! > Therefore in all subsequent GAMESS calculations I was using standard > orientation from Gaussian output (the one above). The results are present= ed > below (using M05/cc-pVDZ and grid(75,302)), together with HF energies, wh= ich > are pretty much reproducible, and M05 calculations using much better than > standard grid (250,974): > Gaussian: > -254.175261128 =A0(InitOr,nosymm) > -254.175313014 =A0(StdOr transformed from InitOr by Gaussian) > GAMESS: > -254.1753800399 (InitOr) > -254.1753738096 (InitOr with "COORD=3DPRINAXIS" keyword) > -254.1753375023 (StdOr) > Grid(250,974): > -254.175301121 =A0(Gaussian, StdOr) > -254.1753365149 (GAMESS, InitOr, "PRINAXIS") > -254.1753372591 (GAMESS, StdOr) > Hartree-Fock: > -252.967151367 =A0(Gaussian) > -252.9671513780 (GAMESS) > > - Many people said that linear dependencies could be the cause. That's ve= ry > unlikely with cc-pVDZ, and there are no linearly dependent MOs present in= my > GAMESS outputs. > - The symmetry is C1 in all cases. > - There are no transition metals present. > - I know that GAMESS interprets CCD keyword as cc-pV(D+d)Z basis set inst= ead > of cc-pVDZ. That's why I was using explicitely defined cc-pVDZ atomic bas= is > set in GAMESS, exactly the one used by Gaussian ("gfinput" switches on > printing of basis set info in Gaussian). > - Another source of error is grid pruning in Gaussian. To avoid this, gri= d > should be requested using e.g. "int(grid=3D75302)" instead of > "int(grid=3Dfinegrid)". There are two weighing schemes available in Gauss= ian. > The scheme of Scuseria and Stratman ("ssweights) is the default, and Beck= e > scheme can be requested using "bweights". I don't have any ideas how > weighing is performed by GAMESS. Unfortunatly changing those options stil= l > does not give similar results: > -254.175313014 =A0(Gaussian - int(grid=3Dfinegrid), ssweights) > -254.175298048 =A0(Gaussian - int(grid=3D75302), ssweights) > -254.175297910 =A0(Gaussian - int(grid=3D75302), bweights) > -254.1753375023 (GAMESS) > I'm afraid hat the whole idea of reproducibility of results is going to f= ail > in case of DFT, but I still hope that it can see the light in the darknes= s. > Somwhere... > Best Regards, > Piotr > On Tue, May 25, 2010 at 7:53 PM, Piotr Nowak piotrnowak[*]student.uw.edu.= pl > wrote: >> >> First of all, thanks everyone for response. Some questions and suggestio= ns >> appeared; I'll try to answer them briefly: >> -I've been using exactly the same structures for the single point energy >> calculations; >> -I have been using spherical harmonics in both programs. Gaussian uses >> them by default, and I have ensured their use in GAMESS with "ISPHER=3D+= 1" >> keyword. The number of cartesian basis fuinctions is the same; >> -Gaussian manual states that default grid uses 75 radial shells and 302 >> angular points/shell. I have been using the same grid in GAMESS thanks t= o >> "NRAD=3D75" and =A0"NLEB=3D302" keywords. I also suspected that grid han= dling >> might be implemented differently in both programs, therefore I tried som= e >> "super-ultra-extra-fine" grid with 250 radial shells and 974 angular >> points/shell (using "Int(Grid=3D250974)" keyword in Gaussian). Unluckily= , the >> energy difference remained within the same order of magnitude as it was = with >> former grid; >> -The relative energies are still different. If you compare e.g. differen= t >> geometries of the same molecule, or activation energies, the error is st= ill >> 10^(-4) hartree. >> I would agree with Soren - there must be some "hidden" adjustable >> parameters, but I have no idea which one can cause these differences. I >> still hope it is possible to get the same results using both programs. >> Kind regards, >> Piotr >> >> On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak >> piotrnowak!^!student.uw.edu.pl wrote: >>> >>> Sent to CCL by: "Piotr =A0Nowak" [piotrnowak~!~student.uw.edu.pl] >>> Dear CCL users, >>> >>> I'm trying to reproduce single point energy obtained with Gaussian 03 >>> using >>> GAMESS US. Hartree-Fock energy is almost exactly the same e.g. >>> Gaussian: -1849.26414782 >>> GAMESS: =A0 -1849.2641478646 >>> >>> Unfortunately my attempts to get the same results using DFT failed. The >>> energy differences between both programs are unreasonably huge. Here ar= e >>> some >>> examples of results for different functionals (the same case as above- >>> mentioned HF example): >>> M05-2X >>> Gaussian: -1855.79754118 >>> GAMESS: =A0 -1855.7976587495 >>> SVWN5 >>> Gaussian: -1845.45112047 >>> GAMESS: =A0 -1845.4510666810 >>> Slater (also known as Dirac, one of the simplest LDA functionals, so I'= m >>> sure >>> it has the same definition in both programs) >>> Gaussian: -1833.20351470 >>> GAMESS: =A0 -1833.2034704727 >>> >>> I have done those calculations using the same grid, using tight >>> convergence >>> criteria. I've found out that Gaussian uses slightly different cc-pVDZ >>> basis >>> set than the one present in Basis Set Exchange, but using this basis se= t >>> with >>> GAMESS has left the results unchanged. I have also tried different >>> guesses, >>> and SCF algorithms, but without success. >>> >>> Here are keywords used in inputs for above calculations. >>> Gaussian: >>> #p m05/cc-pvdz nosymm iop(6/7=3D3) scf=3Dtight >>> >>> GAMESS: >>> =A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END >>> =A0$CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTTYP=3DM05 $END >>> =A0$SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END >>> =A0$SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END >>> =A0$DFT NRAD=3D75 NLEB=3D302 $END >>> >>> I would appreciate any kind of help. >>> Best regards, >>> Piotr Nowak >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> E-mail to subscribers: CHEMISTRY]^[ccl.net or use: >>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >>> >>> E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use >>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml>>> =A0 =A0 =A0http://www.ccl.net/spammers.txt>>> >>> >> >> > > > > -- > http://www.slayer.net/us/orderwpb > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel{:}gmail.com From owner-chemistry@ccl.net Wed May 26 18:42:00 2010 From: "Greg Warren greg=eyesopen.com" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41988-100526150915-31763-HOv3Yg/jXLa7hfxjH5TCJQ * server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 12:08:36 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg^_^eyesopen.com] Dear Fabio, Omega is free if you are an academic or not-for-profit researcher.=20 The web site for applying for an academic license is http://www.eyesopen.com/forms/academic_license_app.php Regards, Greg -----Original Message----- > From: owner-chemistry+greg=3D=3Deyesopen.com[a]ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com[a]ccl.net] On Behalf Of Fabio Molfetta fabioamsc . i= g.com.br Sent: Wednesday, May 26, 2010 8:07 AM To: Greg Warren Subject: CCL: 3D structure generator Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] Are there 3D structure generator programs free of charge to virtual screeni= ng? I kwown that Corina and Omega but these programs are not free. -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 26 19:16:00 2010 From: "Khaled Baaouague baaouague_khaled]^[yahoo.fr" To: CCL Subject: CCL: Re : CCL: Creating surfaces from crystal structures Message-Id: <-41989-100526135150-13895-8P/PoGpA6Jg0qXSWnPawmA*_*server.ccl.net> X-Original-From: Khaled Baaouague Content-Type: multipart/alternative; boundary="0-1688308715-1274896299=:56401" Date: Wed, 26 May 2010 10:51:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Khaled Baaouague [baaouague_khaled^^yahoo.fr] --0-1688308715-1274896299=:56401 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable you can look for CRYSTAL03 or the last last release CRYSTAL09 with the keyw= ord=20 SLABCUT website :http://www.cse.dl.ac.uk/Activity/CRYSTAL or :http://www.crystal.unito.it =A0 Deskins, N Aaron nadeskins-$-WPI.EDU a =E9crit=A0= : De: Deskins, N Aaron nadeskins-$-WPI.EDU Objet: CCL: Creating surfaces from crystal structures =C0: "Baaouague, Khaled " Date: Mercredi 26 mai 2010, 15h00 =A0 Sent to CCL by: "Deskins, N Aaron" [nadeskins a WPI.EDU] Thank you for the responses. GDIS looks like it has real potential. Aaron -----Original Message----- Subject: CCL: Creating surfaces from crystal structures Sent to CCL by: "Nathaniel Aaron Deskins" [nadeskins##wpi.edu] I'm looking for software that will create a surface (i.e. 111 or 110 or wha= tever) from a given bulk crystal structure (from a cif file or some other f= ormat). I'd really like the software to create a surface cell that I can us= e for some periodic simulations.=20 -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=0A=0A=0A --0-1688308715-1274896299=:56401 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
you can look for CRYSTAL03 or the last l= ast release CRYSTAL09 with the keyword
SLABCUT
website :http://www.cse.dl.ac.uk/Activity/CRYSTAL
or :http://www.crystal.unito.it
 
Deskins, N Aaron nadeskins-$-WPI.EDU <owner-chemistry!=!cc= l.net> a =E9crit :

De: Deskins, N Aaron nadeskins-$-WPI.EDU <owne= r-chemistry!=!ccl.net>
Objet: CCL: Creating surfaces from crystal struc= tures
=C0: "Baaouague, Khaled " <baaouague_khaled!=!yahoo.fr>= ;
Date: Mercredi 26 mai 2010, 15h00
 

Sent to CCL by: "Deskins, N Aaron" [nadeskins a = WPI.EDU]
Thank you for the responses. GDIS looks like it has real potent= ial.
Aaron

-----Original Message-----

Subject: CCL: Creati= ng surfaces from crystal structures
Sent to CCL by: "Nathaniel Aaron Des= kins" [nadeskins##wpi.edu]

I'm looking for software that will create= a surface (i.e. 111 or 110 or whatever) from a given bulk crystal structur= e (from a cif file or some other format). I'd really like the software to c= reate a surface cell that I can use for some periodic simulations.

=


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=0A=0A=0A=0A=0A --0-1688308715-1274896299=:56401-- From owner-chemistry@ccl.net Wed May 26 19:52:00 2010 From: "Jeff Woodford jwoodfor%eou.edu" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41990-100526153534-31046-gMJ4SwB2nBbgmQXD9fisEQ{:}server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 May 2010 12:35:36 -0700 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor##eou.edu] Sorry, I sent that last message before reading Piotr's earlier message today. Using the coordinates for 1-fluoroethanol and the SVWN/SVWN5 functional, = I get: HF/cc-pVDZ:=20 GAMESS: -252.9671513705 G03: -252.967151360 SVWN/cc-pVDZ, using the 96,24,48 angular grid: GAMESS: -252.3775843002 G03: -252.377584104 SVWN/cc-pVDZ, using the 96,590 Lebedev grid: GAMESS: -252.3775862124 G03: -252.377584041 SVWN/cc-pVDZ, using the 75,302 Lebedev grid: GAMESS: -252.3775596739 G03: -252.377587390 All of these were with using COORD=3DUNIQUE in GAMESS and using the = default axis parameters in Gaussian. So it seems like there is a problem specifically with the 75,302 Lebedev grid. Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 ________________________________________ > From: owner-chemistry+jwoodfor=3D=3Deou.edu(a)ccl.net [mailto:owner-chemistry+jwoodfor=3D=3Deou.edu(a)ccl.net] On Behalf Of = Piotr Nowak piotrnowak*o*student.uw.edu.pl Sent: Wednesday, May 26, 2010 7:54 AM To: Woodford, Jeffrey N Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Several new plausible solutions to the problems have been made. Because = the problem has been more difficult than I had thought, I've checked those suggestions on a simpler test case, namely: 1-fluoroethanol, using the geometry below: =A0=A0 =A0C =A06 =A0 =A0-1.371551 =A0 -0.189402 =A0 -0.078069 =A0=A0 =A0C =A06 =A0 =A0 0.055735 =A0 -0.002315 =A0 =A00.345325 =A0=A0 =A0H =A01 =A0 =A0-1.765264 =A0 -1.132234 =A0 =A00.321003 =A0=A0 =A0H =A01 =A0 =A0-1.422818 =A0 -0.219081 =A0 -1.174187 =A0=A0 =A0H =A01 =A0 =A0-1.987781 =A0 =A00.640525 =A0 =A00.287358 =A0=A0 =A0O =A08 =A0 =A0 0.815913 =A0 -1.025112 =A0 -0.171888 =A0=A0 =A0H =A01 =A0 =A0 0.154695 =A0 =A00.068673 =A0 =A01.446323 =A0=A0 =A0F =A09 =A0 =A0 0.519096 =A0 =A01.212587 =A0 -0.140203 =A0=A0 =A0H =A01 =A0 =A0 1.716903 =A0 -0.919975 =A0 =A00.152892 - Christopher Cramer suggested that different spatial orientation may = cause different results. The "nosymm" Gaussian keyword indeed suppreses any orientation changes, so input orientation is used throughout the calculations. GAMESS doesn't change the orientation by default, so calculations performed using "nosymm" are made on the same geometry. I = was curious if changing the initial orientation (called "InitOr in the table below - different than the orientation above) to the standard one, can change the results significantly. If "nosymm" is not present, Gaussian rotates the molecule to the standard orientation (StdOr). In order to do = the same using GAMESS, "COORD=3DPRINAXIS" keyword is required. I've found = out that when using standard orientation from the Gaussian output and pasting it = to the GAMESS input (now without "coord=3Dprinaxis), GAMESS gives different result than by rotating the molecule to the principal axis by itself! Therefore in all subsequent GAMESS calculations I was using standard orientation from Gaussian output (the one above). The results are = presented below (using M05/cc-pVDZ and grid(75,302)), together with HF energies, = which are pretty much reproducible, and M05 calculations using much better = than standard grid (250,974): Gaussian: -254.175261128 =A0(InitOr,nosymm) -254.175313014 =A0(StdOr transformed from InitOr by Gaussian) GAMESS: -254.1753800399 (InitOr) -254.1753738096 (InitOr with "COORD=3DPRINAXIS" keyword) -254.1753375023 (StdOr) Grid(250,974): -254.175301121 =A0(Gaussian, StdOr) -254.1753365149 (GAMESS, InitOr, "PRINAXIS") -254.1753372591 (GAMESS, StdOr) Hartree-Fock: -252.967151367 =A0(Gaussian) -252.9671513780 (GAMESS) =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 - Many people said that linear dependencies could be the cause. That's = very unlikely with cc-pVDZ, and there are no linearly dependent MOs present = in my GAMESS outputs.=A0 - The symmetry is C1 in all cases. - There are no transition metals present.=A0 - I know that GAMESS interprets CCD keyword as cc-pV(D+d)Z basis set = instead of cc-pVDZ. That's why I was using explicitely defined cc-pVDZ atomic = basis set in GAMESS, exactly the one used by Gaussian ("gfinput" switches on printing of basis set info in Gaussian). - Another source of error is grid pruning in Gaussian. To avoid this, = grid should be requested using e.g. "int(grid=3D75302)" instead of "int(grid=3Dfinegrid)". There are two weighing schemes available in = Gaussian. The scheme of Scuseria and Stratman ("ssweights) is the default, and = Becke scheme can be requested using "bweights". I don't have any ideas how weighing is performed by GAMESS. Unfortunatly changing those options = still does not give similar results: -254.175313014 =A0(Gaussian - int(grid=3Dfinegrid), ssweights) -254.175298048 =A0(Gaussian - int(grid=3D75302), ssweights) -254.175297910 =A0(Gaussian - int(grid=3D75302), bweights) -254.1753375023 (GAMESS) I'm afraid hat the whole idea of reproducibility of results is going to = fail in case of DFT, but I still hope that it can see the light in the = darkness. Somwhere... Best Regards, Piotr=A0 On Tue, May 25, 2010 at 7:53 PM, Piotr Nowak = piotrnowak[*]student.uw.edu.pl wrote: First of all, thanks everyone for response. Some questions and = suggestions appeared; I'll try to answer them briefly: -I've been using exactly the same structures for the single point energy calculations; -I have been using spherical harmonics in both programs. Gaussian uses = them by default, and I have ensured their use in GAMESS with "ISPHER=3D+1" = keyword. The number of cartesian basis fuinctions is the same; -Gaussian manual states that default grid uses 75 radial shells and 302 angular points/shell. I have been using the same grid in GAMESS thanks = to "NRAD=3D75" and =A0"NLEB=3D302" keywords. I also suspected that grid = handling might be implemented differently in both programs, therefore I tried = some "super-ultra-extra-fine" grid with 250 radial shells and 974 angular points/shell (using "Int(Grid=3D250974)" keyword in Gaussian). = Unluckily, the energy difference remained within the same order of magnitude as it was = with former grid; -The relative energies are still different. If you compare e.g. = different geometries of the same molecule, or activation energies, the error is = still 10^(-4) hartree. I would agree with Soren - there must be some "hidden" adjustable parameters, but I have no idea which one can cause these differences. I still hope it is possible to get the same results using both = programs.=A0 Kind regards, Piotr On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak = piotrnowak!^!student.uw.edu.pl wrote: Sent to CCL by: "Piotr =A0Nowak" [piotrnowak~!~student.uw.edu.pl] Dear CCL users, I'm trying to reproduce single point energy obtained with Gaussian 03 = using GAMESS US. Hartree-Fock energy is almost exactly the same e.g. Gaussian: -1849.26414782 GAMESS: =A0 -1849.2641478646 Unfortunately my attempts to get the same results using DFT failed. The energy differences between both programs are unreasonably huge. Here are some examples of results for different functionals (the same case as above- mentioned HF example): M05-2X Gaussian: -1855.79754118 GAMESS: =A0 -1855.7976587495 SVWN5 Gaussian: -1845.45112047 GAMESS: =A0 -1845.4510666810 Slater (also known as Dirac, one of the simplest LDA functionals, so I'm sure it has the same definition in both programs) Gaussian: -1833.20351470 GAMESS: =A0 -1833.2034704727 I have done those calculations using the same grid, using tight = convergence criteria. I've found out that Gaussian uses slightly different cc-pVDZ = basis set than the one present in Basis Set Exchange, but using this basis set with GAMESS has left the results unchanged. I have also tried different = guesses, and SCF algorithms, but without success. Here are keywords used in inputs for above calculations. Gaussian: #p m05/cc-pvdz nosymm iop(6/7=3D3) scf=3Dtight GAMESS: =A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END =A0$CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTTYP=3DM05 $END =A0$SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END =A0$SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END =A0$DFT NRAD=3D75 NLEB=3D302 $END I would appreciate any kind of help. Best regards, Piotr Nowak -=3D This is automatically added to each message by the mailing script = =3D-=20 E-mail to subscribers: CHEMISTRY]^[ccl.net or use: =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml=A0 =A0 =A0http://www.ccl.net/spammers.txt--=20 http://www.slayer.net/us/orderwpb From owner-chemistry@ccl.net Wed May 26 20:27:00 2010 From: "Brian Salter-Duke brian.james.duke_-_gmail.com" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41991-100526145257-14250-gBGlCMWr09d4LIZANAz9uQ..server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 26 May 2010 19:52:30 +0100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke::gmail.com] Have you asked Mike Schmidt of GAMESS(US) whether the GAMESS results should be identical to Gaussian? On Wed, May 26, 2010 at 04:54:12PM +0200, Piotr Nowak piotrnowak*o*student.uw.edu.pl wrote: > Several new plausible solutions to the problems have been made. Because the > problem has been more difficult than I had thought, I've checked those > suggestions on a simpler test case, namely: 1-fluoroethanol, using the > geometry below: > > C 6 -1.371551 -0.189402 -0.078069 > C 6 0.055735 -0.002315 0.345325 > H 1 -1.765264 -1.132234 0.321003 > H 1 -1.422818 -0.219081 -1.174187 > H 1 -1.987781 0.640525 0.287358 > O 8 0.815913 -1.025112 -0.171888 > H 1 0.154695 0.068673 1.446323 > F 9 0.519096 1.212587 -0.140203 > H 1 1.716903 -0.919975 0.152892 > > - Christopher Cramer suggested that different spatial orientation may cause > different results. The "nosymm" Gaussian keyword indeed suppreses any > orientation changes, so input orientation is used throughout the > calculations. GAMESS doesn't change the orientation by default, so > calculations performed using "nosymm" are made on the same geometry. I was > curious if changing the initial orientation (called "InitOr in the table > below - different than the orientation above) to the standard one, can > change the results significantly. If "nosymm" is not present, Gaussian > rotates the molecule to the standard orientation (StdOr). In order to do the > same using GAMESS, "COORD=PRINAXIS" keyword is required. I've found out that > when using standard orientation from the Gaussian output and pasting it to > the GAMESS input (now without "coord=prinaxis), GAMESS gives different > result than by rotating the molecule to the principal axis by itself! > Therefore in all subsequent GAMESS calculations I was using standard > orientation from Gaussian output (the one above). The results are presented > below (using M05/cc-pVDZ and grid(75,302)), together with HF energies, which > are pretty much reproducible, and M05 calculations using much better than > standard grid (250,974): > > Gaussian: > -254.175261128 (InitOr,nosymm) > -254.175313014 (StdOr transformed from InitOr by Gaussian) > GAMESS: > -254.1753800399 (InitOr) > -254.1753738096 (InitOr with "COORD=PRINAXIS" keyword) > -254.1753375023 (StdOr) > Grid(250,974): > -254.175301121 (Gaussian, StdOr) > -254.1753365149 (GAMESS, InitOr, "PRINAXIS") > -254.1753372591 (GAMESS, StdOr) > Hartree-Fock: > -252.967151367 (Gaussian) > -252.9671513780 (GAMESS) > > - Many people said that linear dependencies could be the cause. That's very > unlikely with cc-pVDZ, and there are no linearly dependent MOs present in my > GAMESS outputs. > - The symmetry is C1 in all cases. > - There are no transition metals present. > - I know that GAMESS interprets CCD keyword as cc-pV(D+d)Z basis set instead > of cc-pVDZ. That's why I was using explicitely defined cc-pVDZ atomic basis > set in GAMESS, exactly the one used by Gaussian ("gfinput" switches on > printing of basis set info in Gaussian). > - Another source of error is grid pruning in Gaussian. To avoid this, grid > should be requested using e.g. "int(grid=75302)" instead of > "int(grid=finegrid)". There are two weighing schemes available in Gaussian. > The scheme of Scuseria and Stratman ("ssweights) is the default, and Becke > scheme can be requested using "bweights". I don't have any ideas how > weighing is performed by GAMESS. Unfortunatly changing those options still > does not give similar results: > -254.175313014 (Gaussian - int(grid=finegrid), ssweights) > -254.175298048 (Gaussian - int(grid=75302), ssweights) > -254.175297910 (Gaussian - int(grid=75302), bweights) > -254.1753375023 (GAMESS) > > I'm afraid hat the whole idea of reproducibility of results is going to fail > in case of DFT, but I still hope that it can see the light in the darkness. > Somwhere... > > Best Regards, > Piotr > > On Tue, May 25, 2010 at 7:53 PM, Piotr Nowak piotrnowak[*]student.uw.edu.pl > wrote: > > > First of all, thanks everyone for response. Some questions and suggestions > > appeared; I'll try to answer them briefly: > > > > -I've been using exactly the same structures for the single point energy > > calculations; > > -I have been using spherical harmonics in both programs. Gaussian uses them > > by default, and I have ensured their use in GAMESS with "ISPHER=+1" keyword. > > The number of cartesian basis fuinctions is the same; > > -Gaussian manual states that default grid uses 75 radial shells and 302 > > angular points/shell. I have been using the same grid in GAMESS thanks to > > "NRAD=75" and "NLEB=302" keywords. I also suspected that grid handling > > might be implemented differently in both programs, therefore I tried some > > "super-ultra-extra-fine" grid with 250 radial shells and 974 angular > > points/shell (using "Int(Grid=250974)" keyword in Gaussian). Unluckily, the > > energy difference remained within the same order of magnitude as it was with > > former grid; > > -The relative energies are still different. If you compare e.g. different > > geometries of the same molecule, or activation energies, the error is still > > 10^(-4) hartree. > > > > I would agree with Soren - there must be some "hidden" adjustable > > parameters, but I have no idea which one can cause these differences. I > > still hope it is possible to get the same results using both programs. > > > > Kind regards, > > Piotr > > > > > > On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piotrnowak!^! > > student.uw.edu.pl > > > wrote: > > > >> > >> Sent to CCL by: "Piotr Nowak" [piotrnowak~!~student.uw.edu.pl] > >> Dear CCL users, > >> > >> I'm trying to reproduce single point energy obtained with Gaussian 03 > >> using > >> GAMESS US. Hartree-Fock energy is almost exactly the same e.g. > >> Gaussian: -1849.26414782 > >> GAMESS: -1849.2641478646 > >> > >> Unfortunately my attempts to get the same results using DFT failed. The > >> energy differences between both programs are unreasonably huge. Here are > >> some > >> examples of results for different functionals (the same case as above- > >> mentioned HF example): > >> M05-2X > >> Gaussian: -1855.79754118 > >> GAMESS: -1855.7976587495 > >> SVWN5 > >> Gaussian: -1845.45112047 > >> GAMESS: -1845.4510666810 > >> Slater (also known as Dirac, one of the simplest LDA functionals, so I'm > >> sure > >> it has the same definition in both programs) > >> Gaussian: -1833.20351470 > >> GAMESS: -1833.2034704727 > >> > >> I have done those calculations using the same grid, using tight > >> convergence > >> criteria. I've found out that Gaussian uses slightly different cc-pVDZ > >> basis > >> set than the one present in Basis Set Exchange, but using this basis set > >> with > >> GAMESS has left the results unchanged. I have also tried different > >> guesses, > >> and SCF algorithms, but without success. > >> > >> Here are keywords used in inputs for above calculations. > >> Gaussian: > >> #p m05/cc-pvdz nosymm iop(6/7=3) scf=tight > >> > >> GAMESS: > >> $BASIS EXTFIL=.TRUE. GBASIS=CCPVDZGN $END > >> $CONTRL ISPHER=+1 SCFTYP=RHF RUNTYP=ENERGY DFTTYP=M05 $END > >> $SYSTEM PARALL=.TRUE. MWORDS=200 $END > >> $SCF DIRSCF=.TRUE. DIIS=.TRUE. $END > >> $DFT NRAD=75 NLEB=302 $END > >> > >> I would appreciate any kind of help. > >> Best regards, > >> Piotr Nowak>> E-mail to subscribers: CHEMISTRY]^[ccl.net or > >> use:>> > >> E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.netor use>> > >> > >> > > > > > > > -- > http://www.slayer.net/us/orderwpb -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke]![bigbond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Wed May 26 21:02:00 2010 From: "Piotr Nowak piotrnowak##student.uw.edu.pl" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41992-100526161448-28878-k06cVCtpm+0C5uOdaYb2Ng|server.ccl.net> X-Original-From: Piotr Nowak Content-Type: multipart/alternative; boundary=0015174c1c0434cfbd048784ec20 Date: Wed, 26 May 2010 22:14:35 +0200 MIME-Version: 1.0 Sent to CCL by: Piotr Nowak [piotrnowak]*[student.uw.edu.pl] --0015174c1c0434cfbd048784ec20 Content-Type: text/plain; charset=ISO-8859-1 It's simply the cc-pVDZ atomic basis set, but defined manually and stored in an external file. Gaussian uses cc-pVDZ basis set which is slightly different than the one available at EMSL Basis Set Exchange and also used by GAMESS. I've copied this basis set from the Gaussian output in order to be absolutely sure that both programs are using exactly the same basis set. The difference is usually quite small (not more than 10^(-9) hartree), but if you have some heavier atoms like chlorine or sulfur and request cc-pVDZ, GAMESS uses cc-pV(D+d)Z basis set instead, with an additional d function on 3rd row atoms, leading to considerable energy differences. If you have your basis set defined manually, you prevent such behaviour. Regards, Piotr On Wed, May 26, 2010 at 6:05 PM, Jeff Woodford jwoodfor|eou.edu < owner-chemistry]![ccl.net> wrote: > > Sent to CCL by: "Jeff Woodford" [jwoodfor(!)eou.edu] > Something I just noticed: > > $BASIS EXTFIL=.TRUE. GBASIS=CCPVDZGN $END > > What is the "CCPVDZGN" basis set and how is it different than the > internally > stored cc-pVDZ basis set in GAMESS or Gaussian 03? > > I think that is the source of your difficulty right there. > > -Jeff > > Jeffrey N. Woodford > Associate Professor of Chemistry > Eastern Oregon University > Tel: 541-962-3321 > Fax: 541-962-3873 > > -----Original Message----- > > From: owner-chemistry+jwoodfor==eou.edu|-|ccl.net > [mailto:owner-chemistry+jwoodfor ==eou.edu|-| > ccl.net] On Behalf Of Gerald > Knizia knizia[#]theochem.uni-stuttgart.de > Sent: Wednesday, May 26, 2010 3:06 AM > To: Woodford, Jeffrey N > Subject: CCL: Different single-point DFT energy between GAMESS and Gaussian > > > Sent to CCL by: Gerald Knizia [knizia.|-|.theochem.uni-stuttgart.de] > On Wednesday 26 May 2010 00:32, Gustavo Mercier gamercier+/-yahoo.comwrote: > > 1. GAMESS direct scf has several short cuts. Look at the control keyword > > group for this. I would get rid of it for both programs. > > Direct SCF is not supposed to cause noticeable changes in the resulting > energy, and certainly not for a SCF method (where the energy error depends > only in second order on the error of the orbitals). > > > 2. DIIS also has adjustable parameters, including how much 'history' > > you keep. > > This impacts only how fast you reach the solution, and in rare unfortunate > cases also which solution you reach (e.g., convergence on a different > minimum > etc). It does not affect the final energy for equivalent solutions. > > > 3. With large basis sets there may be some linear dependencies and the > > programs may automatically make changes in the basis set. Check your > > output. > > cc-pVDZ is not a large basis set. Getting singular overlap matrices with > this > set is pretty much impossible. > > Another thing which actually can cause such discrepancies occurs in > open-shell > systems (namely, the choice of open-shell treatment: restricted open shell > vs > unrestricted open shell vs multi-reference open-shell.). Some programs > might > > default to restricted HF treatments but unrestricted KS treatments (because > spin is a two-particle quantity, and as such is not well-defined in KS > anyway). > > Not even the DF/RI approximation is a good candidate, because this > approximation leads to negligible errors in relative energies when using > decent auxiliary basis sets (e.g., the Weigend ones). > > Different programs really *ARE* supposed to give the same energies for the > same systems. This is one of the things that generally worked very well in > quantum chemistry. > -- > Gerald KniziaJob: > http://www.ccl.net/jobs> > > - This is automatically added to each message by the mailing script -> > > -- http://www.slayer.net/us/orderwpb --0015174c1c0434cfbd048784ec20 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable It's simply the cc-pVDZ atomic basis set, but de= fined manually and stored in an external file. Gaussian uses cc-pVDZ basis = set which is slightly different than the one available at EMSL=A0Basis Set Exchange and also us= ed by GAMESS. I've copied this basis set from the Gaussian output in or= der to be absolutely sure that both programs are using exactly the same bas= is set. The difference is usually quite small (not more than 10^(-9) hartre= e), but if you have some heavier atoms like chlorine or sulfur and request = cc-pVDZ, GAMESS uses cc-pV(D+d)Z basis set instead, with an additional d fu= nction on 3rd row atoms, leading to considerable energy differences. If you= have your basis set defined manually, you prevent such=A0behaviour.=A0

Regards,
Piotr

On Wed, May 26,= 2010 at 6:05 PM, Jeff Woodford jwoodfor|eou.edu= <owner= -chemistry]![ccl.net> wrote:

Sent to CCL by: "Jeff Woodford" [jwoodfor(!)eou.edu]
Something I just noticed:

=A0$BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END

What is the "CCPVDZGN" basis set and how is it different th= an the internally
stored cc-pVDZ basis set in GAMESS or Gaussian 03?

I think that is the source of your difficulty right there.

-Jeff

Jeffrey N. Woodford
Associate Professor of Chemistry
Eastern Oregon University
Tel: 541-962-3321
Fax: 541-962-3873

-----Original Message-----
> From: owner-chemistry+jwoodfor=3D=3Deou.edu|-|ccl.= net
[mailto:owner-chemistry+jwood= for=3D=3Deou.edu|-|ccl.net] On Behalf Of Gerald<= br> Knizia knizia[#]theochem.uni-stuttgart.de
Sent: Wednesday, May 26, 2010 3:06 AM
To: Woodford, Jeffrey N
Subject: CCL: Different single-point DFT energy between GAMESS and Gaussian=


Sent to CCL by: Gerald Knizia [knizia.|-|.theochem.uni-stuttgart.de]
On Wednesday 26 May 2010 00:32, Gustavo Mercier gamercier+/-yahoo.com wrote:
> 1. GAMESS direct scf has several short cuts. Look at the control keywo= rd
> group for this. I would get rid of it for both programs.

Direct SCF is not supposed to cause noticeable changes in the resulting
energy, and certainly not for a SCF method (where the energy error depends<= br> only in second order on the error of the orbitals).

> 2. DIIS also has adjustable parameters, including how much 'histor= y'
> you keep.

This impacts only how fast you reach the solution, and in rare unfortunate<= br> cases also which solution you reach (e.g., convergence on a different
minimum
etc). It does not affect the final energy for equivalent solutions.

> 3. With large basis sets there may be some linear dependencies and the=
> programs may automatically make changes in the basis set. Check your > output.

cc-pVDZ is not a large basis set. Getting singular overlap matrices with this
set is pretty much impossible.

Another thing which actually can cause such discrepancies occurs in
open-shell
systems (namely, the choice of open-shell treatment: restricted open shell<= br> vs
unrestricted open shell vs multi-reference open-shell.). Some programs migh= t

default to restricted HF treatments but unrestricted KS treatments (because=
spin is a two-particle quantity, and as such is not well-defined in KS
anyway).

Not even the DF/RI approximation is a good candidate, because this
approximation leads to negligible errors in relative energies when using decent auxiliary basis sets (e.g., the Weigend ones).

Different programs really *ARE* supposed to give the same energies for the<= br> same systems. This is one of the things that generally worked very well in<= br> quantum chemistry.
--
Gerald Knizia



-=3D This is automatically added to each message by the mailing script =3D-= http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubs= cribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt


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--
http://www.slayer.net/us/orderwpb --0015174c1c0434cfbd048784ec20-- From owner-chemistry@ccl.net Wed May 26 21:37:00 2010 From: "mikko.vainio!A!visipoint.fi" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41993-100526162414-10092-7jb4iJb3bU5U1Mj7msU9vw+/-server.ccl.net> X-Original-From: mikko.vainio],[visipoint.fi Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 26 May 2010 23:24:02 +0300 MIME-Version: 1.0 Sent to CCL by: mikko.vainio- -visipoint.fi Quoting "Fabio Molfetta fabioamsc . ig.com.br" : > > Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] > Are there 3D structure generator programs free of charge to virtual > screening? I kwown that Corina and Omega but these programs are not > free. > Dear Fabio, Balloon is available at no cost from http://users.abo.fi/mivainio/balloon/ It does 2D/3D conversion and conformational analysis. Cheers, Mikko From owner-chemistry@ccl.net Wed May 26 22:12:01 2010 From: "David Hose Anthrax_brothers!^!hotmail.com" To: CCL Subject: CCL:G: enthalpy and entropy value Message-Id: <-41994-100526173434-4806-/8KgMlyzBB8q5RrHIPlmfw.:.server.ccl.net> X-Original-From: "David Hose" Date: Wed, 26 May 2010 17:34:32 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers,,hotmail.com] Mohamed, The Gaussian Thermochemistry White Paper should answer your question. http://www.gaussian.com/g_whitepap/thermo.htm Regards, Dave. ============ CCL:G: enthalpy and entropy value > From: "med mohamed" Subject: CCL:G: enthalpy and entropy value Date: Wed, 26 May 2010 05:38:07 -0400 Sent to CCL by: "med mohamed" [m.maatallah__ucam.ac.ma] Dear colleagues, I would like to know how I can determine the value of the enthalpy and the entropy from a file out obtained from a DFT calculation on gaussian? From owner-chemistry@ccl.net Wed May 26 22:47:00 2010 From: "Michael K. Gilson mgilson.[A].ucsd.edu" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41995-100526200943-29364-omq1S9lBvWE7CUbkuSiEKA[A]server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 May 2010 17:09:06 -0700 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [mgilson%%ucsd.edu] Vconf is also free for academics: http://verachem.com/downloads.html regards Mike On 5/26/2010 12:08 PM, Greg Warren greg=eyesopen.com wrote: > Sent to CCL by: Greg Warren [greg^_^eyesopen.com] > Dear Fabio, > > Omega is free if you are an academic or not-for-profit researcher. > > The web site for applying for an academic license is > > http://www.eyesopen.com/forms/academic_license_app.php > > Regards, > > Greg > > -----Original Message----- > >> From: owner-chemistry+greg==eyesopen.com++ccl.net [mailto:owner-chemistry+greg==eyesopen.com++ccl.net] On Behalf Of Fabio Molfetta fabioamsc . ig.com.br >> > Sent: Wednesday, May 26, 2010 8:07 AM > To: Greg Warren > Subject: CCL: 3D structure generator > > > Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] > Are there 3D structure generator programs free of charge to virtual screening? I kwown that Corina and Omega but these programs are not free.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > - This is automatically added to each message by the mailing script -> > > -- Michael K. Gilson, M.D., Ph.D. Professor Skaggs School of Pharm. U. C. San Diego 9500 Gilman Drive, MC 0736 La Jolla, CA 92093 Voice: 858-822-0622 Fax: 858-822-7726 http://pharmacy.ucsd.edu/labs/gilson/ From owner-chemistry@ccl.net Wed May 26 23:22:00 2010 From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher()us.army.mil" To: CCL Subject: CCL:G: FW: G: Different single-point DFT energy between GAMESS and Gaussian (UNCLASSIFIED) Message-Id: <-41996-100526154338-9021-jXWX68X0CPz1rTdhhIOIgg{}server.ccl.net> X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 15:42:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher%a%us.army.mil] Classification: UNCLASSIFIED Caveats: NONE Dear Piotr, The errors between Gaussian and Gamess are on the same level as the errors within Gaussian or Gamess, ~10^-4 a.u. Unless you believe that M05 produces subchemical accuracy these results are the same for all chemical intents and purposes. Also M05 contains a slew of parameters. Do you find the same discrepancies with "simpler" functionals (BLYP, B3LYP, PBE, PBE0)? Sincerely, Christopher -----Original Message----- Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Several new plausible solutions to the problems have been made. Because the problem has been more difficult than I had thought, I've checked those suggestions on a simpler test case, namely: 1-fluoroethanol, using the geometry below: C 6 -1.371551 -0.189402 -0.078069 C 6 0.055735 -0.002315 0.345325 H 1 -1.765264 -1.132234 0.321003 H 1 -1.422818 -0.219081 -1.174187 H 1 -1.987781 0.640525 0.287358 O 8 0.815913 -1.025112 -0.171888 H 1 0.154695 0.068673 1.446323 F 9 0.519096 1.212587 -0.140203 H 1 1.716903 -0.919975 0.152892 - Christopher Cramer suggested that different spatial orientation may cause different results. The "nosymm" Gaussian keyword indeed suppreses any orientation changes, so input orientation is used throughout the calculations. GAMESS doesn't change the orientation by default, so calculations performed using "nosymm" are made on the same geometry. I was curious if changing the initial orientation (called "InitOr in the table below - different than the orientation above) to the standard one, can change the results significantly. If "nosymm" is not present, Gaussian rotates the molecule to the standard orientation (StdOr). In order to do the same using GAMESS, "COORD=3DPRINAXIS" keyword is = required. I've found out that when using standard orientation from the Gaussian output and pasting it to the GAMESS input (now without = "coord=3Dprinaxis), GAMESS gives different result than by rotating the molecule to the principal axis by itself! Therefore in all subsequent GAMESS calculations I was using standard orientation from Gaussian output (the one above). The results are presented below (using M05/cc-pVDZ and grid(75,302)), together with HF energies, which are pretty much reproducible, and M05 calculations using much better than standard grid (250,974): Gaussian: -254.175261128 (InitOr,nosymm) -254.175313014 (StdOr transformed from InitOr by Gaussian) GAMESS: -254.1753800399 (InitOr) -254.1753738096 (InitOr with "COORD=3DPRINAXIS" keyword) -254.1753375023 (StdOr) Grid(250,974): -254.175301121 (Gaussian, StdOr) -254.1753365149 (GAMESS, InitOr, "PRINAXIS") -254.1753372591 (GAMESS, StdOr) Hartree-Fock: -252.967151367 (Gaussian) -252.9671513780 (GAMESS) =20 - Many people said that linear dependencies could be the cause. That's very unlikely with cc-pVDZ, and there are no linearly dependent MOs present in my GAMESS outputs.=20 - The symmetry is C1 in all cases. - There are no transition metals present.=20 - I know that GAMESS interprets CCD keyword as cc-pV(D+d)Z basis set instead of cc-pVDZ. That's why I was using explicitely defined cc-pVDZ atomic basis set in GAMESS, exactly the one used by Gaussian ("gfinput" switches on printing of basis set info in Gaussian). - Another source of error is grid pruning in Gaussian. To avoid this, grid should be requested using e.g. "int(grid=3D75302)" instead of "int(grid=3Dfinegrid)". There are two weighing schemes available in Gaussian. The scheme of Scuseria and Stratman ("ssweights) is the default, and Becke scheme can be requested using "bweights". I don't have any ideas how weighing is performed by GAMESS. Unfortunatly changing those options still does not give similar results: -254.175313014 (Gaussian - int(grid=3Dfinegrid), ssweights) -254.175298048 (Gaussian - int(grid=3D75302), ssweights) -254.175297910 (Gaussian - int(grid=3D75302), bweights) -254.1753375023 (GAMESS) I'm afraid hat the whole idea of reproducibility of results is going to fail in case of DFT, but I still hope that it can see the light in the darkness. Somwhere... Best Regards, Piotr=20 On Tue, May 25, 2010 at 7:53 PM, Piotr Nowak piotrnowak[*]student.uw.edu.pl wrote: First of all, thanks everyone for response. Some questions and suggestions appeared; I'll try to answer them briefly: -I've been using exactly the same structures for the single point energy calculations; -I have been using spherical harmonics in both programs. Gaussian uses them by default, and I have ensured their use in GAMESS with "ISPHER=3D+1" keyword. The number of cartesian basis fuinctions is the same; -Gaussian manual states that default grid uses 75 radial shells and 302 angular points/shell. I have been using the same grid in GAMESS thanks to "NRAD=3D75" and "NLEB=3D302" keywords. I also suspected that = grid handling might be implemented differently in both programs, therefore I tried some "super-ultra-extra-fine" grid with 250 radial shells and 974 angular points/shell (using "Int(Grid=3D250974)" keyword in Gaussian). Unluckily, the energy difference remained within the same order of magnitude as it was with former grid; -The relative energies are still different. If you compare e.g. different geometries of the same molecule, or activation energies, the error is still 10^(-4) hartree. I would agree with Soren - there must be some "hidden" adjustable parameters, but I have no idea which one can cause these differences. I still hope it is possible to get the same results using both programs.=20 Kind regards, Piotr =09 On Tue, May 25, 2010 at 12:50 AM, Piotr Nowak piotrnowak!^!student.uw.edu.pl > wrote: =09 Sent to CCL by: "Piotr Nowak" [piotrnowak~!~student.uw.edu.pl] Dear CCL users, =09 I'm trying to reproduce single point energy obtained with Gaussian 03 using GAMESS US. Hartree-Fock energy is almost exactly the same e.g. Gaussian: -1849.26414782 GAMESS: -1849.2641478646 =09 Unfortunately my attempts to get the same results using DFT failed. The energy differences between both programs are unreasonably huge. Here are some examples of results for different functionals (the same case as above- mentioned HF example): M05-2X Gaussian: -1855.79754118 GAMESS: -1855.7976587495 SVWN5 Gaussian: -1845.45112047 GAMESS: -1845.4510666810 Slater (also known as Dirac, one of the simplest LDA functionals, so I'm sure it has the same definition in both programs) Gaussian: -1833.20351470 GAMESS: -1833.2034704727 =09 I have done those calculations using the same grid, using tight convergence criteria. I've found out that Gaussian uses slightly different cc-pVDZ basis set than the one present in Basis Set Exchange, but using this basis set with GAMESS has left the results unchanged. I have also tried different guesses, and SCF algorithms, but without success. =09 Here are keywords used in inputs for above calculations. Gaussian: #p m05/cc-pvdz nosymm iop(6/7=3D3) scf=3Dtight =09 GAMESS: $BASIS EXTFIL=3D.TRUE. GBASIS=3DCCPVDZGN $END $CONTRL ISPHER=3D+1 SCFTYP=3DRHF RUNTYP=3DENERGY DFTTYP=3DM05 $END $SYSTEM PARALL=3D.TRUE. MWORDS=3D200 $END $SCF DIRSCF=3D.TRUE. DIIS=3D.TRUE. $END $DFT NRAD=3D75 NLEB=3D302 $END =09 I would appreciate any kind of help. Best regards, Piotr Nowak =09 =09 =09 -=3D This is automatically added to each message by the mailing script =3D-=20 =09 E-mail to subscribers: CHEMISTRY]^[ccl.net or use:=20 =09 E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use=20 =09http://www.ccl.net/chemistry/sub_unsub.shtml =20 =09=20 =09=20=20 =09=20 =09=20 =09=20 =09 =09 =09 --=20 http://www.slayer.net/us/orderwpb =20 Classification: UNCLASSIFIED Caveats: NONE