From owner-chemistry@ccl.net Fri Jan 21 04:51:01 2011 From: "Krishna Govender kk.govender_._gmail.com" To: CCL Subject: CCL:G: Integrals from DFT simulations Message-Id: <-43716-110121044854-16507-TDTFEWJpvWhwVS5fwrWTdQ]|[server.ccl.net> X-Original-From: "Krishna Govender" Date: Fri, 21 Jan 2011 04:48:51 -0500 Sent to CCL by: "Krishna Govender" [kk.govender ~ gmail.com] Good day everyone. I hope that someone might be able to assist me with a problem I am currently experiencing. I have run some DFT simulations of some fairly simple systems and I wish to determine the one and two-center integral terms for the DFT optimized structures. Where would I be able to find the above mentioned terms? These terms don't seem to be located within the Gaussian log file. Do I need to write out an additional file to get these terms? If so, what file do I need to write out? Will the file that is written out be in binary? If so, how may I be able to convert the binary file into a readable format? I would appreciate any input on the matter. Thanks in advance. Krishna Govender Department of Chemistry Scientific Computing Research Unit University of Cape Town From owner-chemistry@ccl.net Fri Jan 21 08:30:00 2011 From: "David Mannock dmannock/./ualberta.ca" To: CCL Subject: CCL:G: Gaussian on Centos? Message-Id: <-43717-110121041900-5005-kuKb8zVL7wTJa5dpjg0yDw:server.ccl.net> X-Original-From: David Mannock Content-Type: multipart/alternative; boundary="------------080206010008040205060506" Date: Fri, 21 Jan 2011 02:18:24 -0700 MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock##ualberta.ca] This is a multi-part message in MIME format. --------------080206010008040205060506 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dan, That link is for GV3.0X. GV5 is multiplatform and is a big improvement on earlier versions. Try it with Ubuntu 10.04 and see if it works. Dave On 1/20/2011 4:06 PM, Jason Swails swails%qtp.ufl.edu wrote: > > > On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com > > wrote: > > Hi Daniel, > > Both Gaussian and Gaussview will run on CentOS; I've got it > working on an Altix XE310 in my lab. A word of warning, though; if > you get Gaussview, it will only run on CentOS or Redhat. It > doesn't run on Ubuntu, or any other open-source Linux flavor > (easily, at least). > > > ooh! A challenge! Were it not for the hefty price tag I'd give it a > go. An ubuntu thread that may be helpful: > http://ubuntuforums.org/showthread.php?t=634578 > > In any case, Linux is Linux, so I can't imagine it's completely > incompatible with other flavors. It may be necessary to install > additional packages with the proper library versions. > > As a side-note, SUSE 10 is listed as a supported platform if an > additional package is installed. > > All the best, > Jason > > > > Be well, > > Jason > > Jason S. D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > > On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu > > wrote: > > > Sent to CCL by: Daniel Strahs [dstrahs**pace.edu > ] > Hello colleagues: > > Has any one had any experience installing Gaussian for > Linux/Red Hat > Enterprise on the Centos OS? The binary compatibility with RedHat > interests us. > > Thanks for any responses! > > -- > Daniel B. Strahs > Associate Professor > Biology and Health Sciences Department > Pace University, New York > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY],[ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 --------------080206010008040205060506 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dan, That link is for GV3.0X. GV5 is multiplatform and is a big improvement on earlier versions. Try it with Ubuntu 10.04 and see if it works. Dave

On 1/20/2011 4:06 PM, Jason Swails swails%qtp.ufl.edu wrote:


On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com <owner-chemistry(_)ccl.net> wrote:
Hi Daniel,

Both Gaussian and Gaussview will run on CentOS; I've got it working on an Altix XE310 in my lab. A word of warning, though; if you get Gaussview, it will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other open-source Linux flavor (easily, at least).

ooh! A challenge!  Were it not for the hefty price tag I'd give it a go.  An ubuntu thread that may be helpful:  http://ubuntuforums.org/showthread.php?t=634578

In any case, Linux is Linux, so I can't imagine it's completely incompatible with other flavors.  It may be necessary to install additional packages with the proper library versions.

As a side-note, SUSE 10 is listed as a supported platform if an additional package is installed.

All the best,
Jason



Be well,

Jason

Jason S. D'Acchioli
Assistant Professor of Chemistry
University of Wisconsin-Stevens Point

On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: Daniel Strahs [dstrahs**pace.edu]
Hello colleagues:

Has any one had any experience installing Gaussian for Linux/Red Hat
Enterprise on the Centos OS? The binary compatibility with RedHat
interests us.

Thanks for any responses!

--
Daniel B. Strahs
Associate Professor
Biology and Health Sciences Department
Pace University, New York


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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
--------------080206010008040205060506-- From owner-chemistry@ccl.net Fri Jan 21 09:05:00 2011 From: "bella A aloysius.bella=-=gmail.com" To: CCL Subject: CCL: Chemistry Message-Id: <-43718-110121071824-30839-ZhcOyNEMt7ZcUhuppo7I5w::server.ccl.net> X-Original-From: "bella A" Date: Fri, 21 Jan 2011 07:18:23 -0500 Sent to CCL by: "bella A" [aloysius.bella%a%gmail.com] Hello, I am a beginner to computational chemistry. In TDDFT calculations, the output screen shows the below type of data. my question is, From this how to find out which is which type of transition (i.e pi to pi* or n to pi* transitions etc). what is f value? what does it mean? How to interpret this data.Kindly answer anyone. lot of thanks in advance. Excitation energies and oscillator strengths: Excited State 1: Singlet-A" 2.3889 eV 519.00 nm f=0.0000 =0.000 20 -> 21 0.70736 Excited State 2: Singlet-A" 5.2913 eV 234.32 nm f=0.0658 =0.000 20 -> 22 0.70039 Excited State 3: Singlet-A' 5.4509 eV 227.46 nm f=0.1919 =0.000 19 -> 21 0.67529 20 -> 23 -0.16647 Excited State 4: Singlet-A' 6.0392 eV 205.30 nm f=0.0056 =0.000 18 -> 21 0.70346 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -515.886026542 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 5: Singlet-A" 6.2394 eV 198.71 nm f=0.0450 =0.000 20 -> 24 0.67261 20 -> 26 0.13843 20 -> 27 -0.12877 Excited State 6: Singlet-A' 6.2572 eV 198.15 nm f=0.0695 =0.000 19 -> 21 0.16021 20 -> 23 0.68481 Excited State 7: Singlet-A" 6.3040 eV 196.68 nm f=0.0009 =0.000 20 -> 24 -0.16851 20 -> 25 0.30226 20 -> 26 0.59888 20 -> 27 -0.12727 Excited State 8: Singlet-A" 6.3992 eV 193.75 nm f=0.0008 =0.000 20 -> 25 0.62984 20 -> 26 -0.29793 Excited State 9: Singlet-A" 6.7285 eV 184.27 nm f=0.0016 =0.000 20 -> 26 0.16944 20 -> 27 0.67559 Excited State 10: Singlet-A' 6.8632 eV 180.65 nm f=0.0778 =0.000 20 -> 28 0.70048 A. Bella aloysius.bella(!)gmail.com From owner-chemistry@ccl.net Fri Jan 21 09:41:00 2011 From: "yang guo guoyang0123-*-gmail.com" To: CCL Subject: CCL:G: lanl2dz basis set: GAMESS vs G09 Message-Id: <-43719-110120221019-15487-YRhPAYxm/xGGuQh9ZPYsiQ%a%server.ccl.net> X-Original-From: yang guo Content-Type: multipart/alternative; boundary=0016e64982d0b86c12049a5295dd Date: Fri, 21 Jan 2011 11:09:56 +0800 MIME-Version: 1.0 Sent to CCL by: yang guo [guoyang0123 ~~ gmail.com] --0016e64982d0b86c12049a5295dd Content-Type: text/plain; charset=ISO-8859-1 As far as I know, it is very common that the basis set with the same name in G09 and Gamess are different. Even the STO-3G basis set of Mg atom is different. You can use the key word 'Punch' in Gaussian to generate Gamess input file, if you want get the same result. And this website may give you some help: https://bse.pnl.gov/bse/portal 2011/1/21 Cheri Ann McFerrin cmcfer1..lsu.edu > > Sent to CCL by: "Cheri Ann McFerrin" [cmcfer1{:}lsu.edu] > Hi Everyone: > > The Lanl2dz basis for Copper at the EMSL basis set exchange (pnl.gov) in > GAMESS-US format versus > the Lanl2dz basis for Copper using G09 are different. I am copying the > coefficients & exponents > here for convenience, separated by asterisks. Can anyone tell me why the > Lanl2dz basis is not > consistent with respect to GAMESS & G09? We are getting different > equilibrium geometries and > eneriges as a result. > > Thank you!! > > Dr. Cheri McFerrin, LSU Dept of Chemistry, Baton Rouge, LA USA > > *********************************************************************************** > ! LANL2DZ ECP EMSL Basis Set Exchange Library 1/20/11 10:05 AM > ! Elements References > ! -------- ---------- > ! H - Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Electronic > Structure > ! Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRESS (1977) > ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). > ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). > ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). > $DATA > COPPER > S 3 > 1 8.1760000 -0.4210260 > 2 2.5680000 0.7385924 > 3 0.9587000 0.5525692 > S 4 > 1 8.1760000 0.1787665 > 2 2.5680000 -0.3592273 > 3 0.9587000 -0.4704825 > 4 0.1153000 1.0807407 > S 1 > 1 0.0396000 1.0000000 > P 3 > 1 25.6300000 -0.0489173 > 2 3.1660000 0.6272854 > 3 1.0230000 0.4716188 > P 1 > 1 0.0860000 1.0000000 > P 1 > 1 0.0240000 1.0000000 > D 4 > 1 41.3400000 0.0465424 > 2 11.4200000 0.2227824 > 3 3.8390000 0.4539059 > 4 1.2300000 0.5314769 > D 1 > 1 0.3102000 1.0000000 > $END > ! Elements References > ! -------- ---------- > ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). > ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). > ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). > $ECP > CU-ECP GEN 10 2 > 3 ----- d potential ----- > -10.0000000 1 511.9951763 > -72.5548282 2 93.2801074 > -12.7450231 2 23.2206669 > 4 ----- s-d potential ----- > 3.0000000 0 173.1180854 > 23.8351825 1 185.2419886 > 473.8930488 2 73.1517847 > 157.6345823 2 14.6884157 > 4 ----- p-d potential ----- > 5.0000000 0 100.7191369 > 6.4990936 1 130.8345665 > 351.4605395 2 53.8683720 > 85.5016036 2 14.0989469 > $END > *********************from G09 output after using lanl2dz > 6d********************************* > S 3 1.00 0.000000000000 > 0.2568000000D+01 -0.4632439327D-01 > 0.9587000000D+00 -0.2394893745D+00 > 0.1153000000D+00 0.1097356778D+01 > S 3 1.00 0.000000000000 > 0.8176000000D+01 -0.4210259893D+00 > 0.2568000000D+01 0.7385923813D+00 > 0.9587000000D+00 0.5525691860D+00 > S 1 1.00 0.000000000000 > 0.3960000000D-01 0.1000000000D+01 > P 3 1.00 0.000000000000 > 0.2563000000D+02 -0.4891730019D-01 > 0.3166000000D+01 0.6272854025D+00 > 0.1023000000D+01 0.4716188019D+00 > P 1 1.00 0.000000000000 > 0.8600000000D-01 0.1000000000D+01 > P 1 1.00 0.000000000000 > 0.2400000000D-01 0.1000000000D+01 > D 4 1.00 0.000000000000 > 0.4134000000D+02 0.4654240160D-01 > 0.1142000000D+02 0.2227824077D+00 > 0.3839000000D+01 0.4539059156D+00 > 0.1230000000D+01 0.5314769183D+00 > D 1 1.00 0.000000000000 > 0.3102000000D+00 0.1000000000D+01 > **************************************************************> > > --0016e64982d0b86c12049a5295dd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
As far as I know, it is very common that the basis set with the same n= ame in G09 and Gamess are different.=A0Even the STO-3G basis=A0set of=A0Mg = atom=A0is different.=A0 You can use the key word 'Punch' in Gaussia= n to generate Gamess input file, if you want get the same result. And this = website may give you some help: = https://bse.pnl.gov/bse/portal

2011/1/21 Cheri Ann McFerrin cmcfer1..lsu.edu <owner-chemistry-#-ccl.net>

Sent to CCL by: "Cheri = Ann McFerrin" [cmcfer1{:}lsu.edu]
Hi Everyone:

The Lanl2dz basis for Copper at the EMSL basis set exch= ange (pnl.gov) in GAMESS-= US format versus
the Lanl2dz basis for Copper using G09 are different. = =A0I am copying the coefficients & exponents
here for convenience, separated by asterisks. =A0Can anyone tell me why the= Lanl2dz basis is not
consistent with respect to GAMESS & G09? =A0We= are getting different equilibrium geometries and
eneriges as a result.<= br>
Thank you!!

Dr. Cheri McFerrin, LSU Dept of Chemistry, Baton Rou= ge, LA USA
*************************************************************= **********************
! =A0LANL2DZ ECP =A0EMSL =A0Basis Set Exchange Li= brary =A0 1/20/11 10:05 AM
! Elements =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Referenc= es
! -------- =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 --= --------
! H =A0- Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Ele= ctronic Structure
! Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRES= S (1977)
! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! P.= J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
! P. J. Hay and W= . R. Wadt, J. Chem. Phys. 82, 299 (1985).
$DATA
COPPER
S =A0 3
=A01 =A0 =A0 =A08.1760000 =A0 =A0 =A0 =A0 =A0 =A0 -0.4210260
=A02 =A0 = =A0 =A02.5680000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.7385924
=A03 =A0 =A0 =A00.= 9587000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.5525692
S =A0 4
=A01 =A0 =A0 =A0= 8.1760000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.1787665
=A02 =A0 =A0 =A02.5680000= =A0 =A0 =A0 =A0 =A0 =A0 -0.3592273
=A03 =A0 =A0 =A00.9587000 =A0 =A0 =A0 =A0 =A0 =A0 -0.4704825
=A04 =A0 = =A0 =A00.1153000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.0807407
S =A0 1
=A01 = =A0 =A0 =A00.0396000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.0000000
P =A0 3
=A0= 1 =A0 =A0 25.6300000 =A0 =A0 =A0 =A0 =A0 =A0 -0.0489173
=A02 =A0 =A0 =A0= 3.1660000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.6272854
=A03 =A0 =A0 =A01.0230000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.4716188
P =A0 1=A01 =A0 =A0 =A00.0860000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.0000000
P =A0 1=
=A01 =A0 =A0 =A00.0240000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.0000000
D =A0= 4
=A01 =A0 =A0 41.3400000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.0465424
=A02 = =A0 =A0 11.4200000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.2227824
=A03 =A0 =A0 =A03.8390000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.4539059
=A04 =A0 = =A0 =A01.2300000 =A0 =A0 =A0 =A0 =A0 =A0 =A00.5314769
D =A0 1
=A01 = =A0 =A0 =A00.3102000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.0000000
$END
! Elem= ents =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 References
= ! -------- =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 --------= --
! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! = =A0 =A0 =A0 =A0 =A0P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).=
! =A0 =A0 =A0 =A0 =A0P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (= 1985).
=A0$ECP
=A0CU-ECP GEN =A0 =A0 10 =A0 =A0 2
=A03 =A0 =A0 =A0----- d potential =A0= =A0 -----
=A0 =A0-10.0000000 =A0 =A0 =A0 =A01 =A0 =A0511.9951763
=A0= =A0-72.5548282 =A0 =A0 =A0 =A02 =A0 =A0 93.2801074
=A0 =A0-12.7450231 = =A0 =A0 =A0 =A02 =A0 =A0 23.2206669
=A04 =A0 =A0 =A0----- s-d potential = =A0 =A0 -----
=A0 =A0 =A03.0000000 =A0 =A0 =A0 =A00 =A0 =A0173.1180854
=A0 =A0 23.8351= 825 =A0 =A0 =A0 =A01 =A0 =A0185.2419886
=A0 =A0473.8930488 =A0 =A0 =A0 = =A02 =A0 =A0 73.1517847
=A0 =A0157.6345823 =A0 =A0 =A0 =A02 =A0 =A0 14.6= 884157
=A04 =A0 =A0 =A0----- p-d potential =A0 =A0 -----
=A0 =A0 =A05= .0000000 =A0 =A0 =A0 =A00 =A0 =A0100.7191369
=A0 =A0 =A06.4990936 =A0 =A0 =A0 =A01 =A0 =A0130.8345665
=A0 =A0351.4605= 395 =A0 =A0 =A0 =A02 =A0 =A0 53.8683720
=A0 =A0 85.5016036 =A0 =A0 =A0 = =A02 =A0 =A0 14.0989469
=A0$END
*********************from G09 output = after using lanl2dz 6d*********************************
=A0S =A0 3 1.00 =A0 =A0 =A0 0.000000000000
=A0 =A0 =A00.2568000000D+01 -= 0.4632439327D-01
=A0 =A0 =A00.9587000000D+00 -0.2394893745D+00
=A0 = =A0 =A00.1153000000D+00 =A00.1097356778D+01
=A0S =A0 3 1.00 =A0 =A0 =A0 = 0.000000000000
=A0 =A0 =A00.8176000000D+01 -0.4210259893D+00
=A0 =A0 =A00.2568000000D+01 =A00.7385923813D+00
=A0 =A0 =A00.9587000000D= +00 =A00.5525691860D+00
=A0S =A0 1 1.00 =A0 =A0 =A0 0.000000000000
= =A0 =A0 =A00.3960000000D-01 =A00.1000000000D+01
=A0P =A0 3 1.00 =A0 =A0 = =A0 0.000000000000
=A0 =A0 =A00.2563000000D+02 -0.4891730019D-01
=A0 =A0 =A00.3166000000D+01 =A00.6272854025D+00
=A0 =A0 =A00.1023000000D= +01 =A00.4716188019D+00
=A0P =A0 1 1.00 =A0 =A0 =A0 0.000000000000
= =A0 =A0 =A00.8600000000D-01 =A00.1000000000D+01
=A0P =A0 1 1.00 =A0 =A0 = =A0 0.000000000000
=A0 =A0 =A00.2400000000D-01 =A00.1000000000D+01
=A0D =A0 4 1.00 =A0 =A0 =A0 0.000000000000
=A0 =A0 =A00.4134000000D+02 = =A00.4654240160D-01
=A0 =A0 =A00.1142000000D+02 =A00.2227824077D+00
= =A0 =A0 =A00.3839000000D+01 =A00.4539059156D+00
=A0 =A0 =A00.1230000000D= +01 =A00.5314769183D+00
=A0D =A0 1 1.00 =A0 =A0 =A0 0.000000000000
=A0 =A0 =A00.3102000000D+00 =A00.1000000000D+01
************************= **************************************



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--0016e64982d0b86c12049a5295dd-- From owner-chemistry@ccl.net Fri Jan 21 10:14:00 2011 From: "Jim Kress ccl_nospam-*-kressworks.com" To: CCL Subject: CCL: Chemistry Message-Id: <-43720-110121095723-21725-3RpsV2yi+fftzOctASjPbg_-_server.ccl.net> X-Original-From: "Jim Kress" Date: Fri, 21 Jan 2011 09:57:20 -0500 Sent to CCL by: "Jim Kress" [ccl_nospam- -kressworks.com] If you use NBO on your system, it will automatically classify all the orbitals with respect to their sigma, pi, n - bonding and antibonding (*) characteristics. Then you will automatically be able to find the information you desire, since you have the orbital numbers. http://www.chem.wisc.edu/~nbo5/ Jim From owner-chemistry@ccl.net Fri Jan 21 11:03:00 2011 From: "Eduard Matito ematito()gmail.com" To: CCL Subject: CCL:G: Integrals from DFT simulations Message-Id: <-43721-110121091238-6635-c1PLnQheUq39p9dpi+QvIQ(a)server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 21 Jan 2011 15:12:04 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito*gmail.com] Check IOP(3/33). See the iop manual: http://www.gaussian.com/g_tech/g_iops/ov3.htm Best, Eduard On Jan 21, 2011, at 10:48 AM, Krishna Govender kk.govender_._gmail.com wrote: > > Sent to CCL by: "Krishna Govender" [kk.govender ~ gmail.com] > Good day everyone. > > I hope that someone might be able to assist me with a problem I am > currently experiencing. > I have run some DFT simulations of some fairly simple systems and I > wish to determine the one and two-center integral terms for the DFT > optimized structures. > > Where would I be able to find the above mentioned terms? These terms > don't seem to be located within the Gaussian log file. > Do I need to write out an additional file to get these terms? If so, > what file do I need to write out? > Will the file that is written out be in binary? If so, how may I be > able to convert the binary file into a readable format? > > I would appreciate any input on the matter. > Thanks in advance. > > Krishna Govender > Department of Chemistry > Scientific Computing Research Unit > University of Cape Town > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > -- Eduard Matito Postdoctoral researcher Institute of Physics University of Szczecin Wielkopolska 15 70451 Szczecin (Poland) Phone: +48914441436 http://ematito.webs.com From owner-chemistry@ccl.net Fri Jan 21 11:38:01 2011 From: "Jim Kress ccl_nospam###kressworks.com" To: CCL Subject: CCL: Chemistry Message-Id: <-43722-110121095245-16903-R8K9N5rHGN6PotM3Y4j8wA .. server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 21 Jan 2011 09:52:09 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam---kressworks.com] If you use NBO on your system, it will automatically classify all the orbitals with respect to their sigma, pi, n - bonding and antibonding (*) characteristics. Then you will automatically be able to find the information you desire, since you have the orbital numbers. http://www.chem.wisc.edu/~nbo5/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com * ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com * ccl.net] On Behalf Of bella A > aloysius.bella=-=gmail.com > Sent: Friday, January 21, 2011 7:18 AM > To: Kress, Jim > Subject: CCL: Chemistry > > > Sent to CCL by: "bella A" [aloysius.bella%a%gmail.com] > Hello, > I am a beginner to computational chemistry. In TDDFT calculations, the > output screen shows the below type of data. my question is, > From this how to find out which is which type of > transition (i.e pi to pi* or n to pi* transitions etc). > what is f value? what does it mean? > How to interpret this data.Kindly answer anyone. > lot of thanks in advance. > > > > > > Excitation energies and oscillator strengths: > > Excited State 1: Singlet-A" 2.3889 eV 519.00 nm f=0.0000 > =0.000 > 20 -> 21 0.70736 > > Excited State 2: Singlet-A" 5.2913 eV 234.32 nm f=0.0658 > =0.000 > 20 -> 22 0.70039 > > Excited State 3: Singlet-A' 5.4509 eV 227.46 nm f=0.1919 > =0.000 > 19 -> 21 0.67529 > 20 -> 23 -0.16647 > > Excited State 4: Singlet-A' 6.0392 eV 205.30 nm f=0.0056 > =0.000 > 18 -> 21 0.70346 > This state for optimization and/or second-order correction. > Total Energy, E(TD-HF/TD-KS) = -515.886026542 > Copying the excited state density for this state as the 1-particle > RhoCI density. > > Excited State 5: Singlet-A" 6.2394 eV 198.71 nm f=0.0450 > =0.000 > 20 -> 24 0.67261 > 20 -> 26 0.13843 > 20 -> 27 -0.12877 > > Excited State 6: Singlet-A' 6.2572 eV 198.15 nm f=0.0695 > =0.000 > 19 -> 21 0.16021 > 20 -> 23 0.68481 > > Excited State 7: Singlet-A" 6.3040 eV 196.68 nm f=0.0009 > =0.000 > 20 -> 24 -0.16851 > 20 -> 25 0.30226 > 20 -> 26 0.59888 > 20 -> 27 -0.12727 > > Excited State 8: Singlet-A" 6.3992 eV 193.75 nm f=0.0008 > =0.000 > 20 -> 25 0.62984 > 20 -> 26 -0.29793 > > Excited State 9: Singlet-A" 6.7285 eV 184.27 nm f=0.0016 > =0.000 > 20 -> 26 0.16944 > 20 -> 27 0.67559 > > Excited State 10: Singlet-A' 6.8632 eV 180.65 nm f=0.0778 > =0.000 > 20 -> 28 0.70048 > > > A. Bella > aloysius.bella_-_gmail.com> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Fri Jan 21 12:13:00 2011 From: "Jim Kress ccl_nospam,,kressworks.com" To: CCL Subject: CCL:G: lanl2dz basis set: GAMESS vs G09 Message-Id: <-43723-110121120346-29725-TQG0Wh3ZoJEEHk3aykjpKw|*|server.ccl.net> X-Original-From: "Jim Kress" Date: Fri, 21 Jan 2011 12:03:43 -0500 Sent to CCL by: "Jim Kress" [ccl_nospam{:}kressworks.com] So, your claim is that Gaussian has unilaterally redefined the basis sets for many atoms but retained their common name? That makes no sense. Jim Kress From owner-chemistry@ccl.net Fri Jan 21 12:48:00 2011 From: "Jim Kress ccl_nospam-.-kressworks.com" To: CCL Subject: CCL:G: lanl2dz basis set: GAMESS vs G09 Message-Id: <-43724-110121113606-4574-l0mAsGbz4j5ZiLsEb4jP5A .. server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01CBB95F.42A1C200" Date: Fri, 21 Jan 2011 11:35:07 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam/a\kressworks.com] This is a multi-part message in MIME format. ------=_NextPart_000_000D_01CBB95F.42A1C200 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit So, your claim is that Gaussian has unilaterally redefined the basis sets for many atoms but retained their common name? That makes no sense. Jim Kress > From: owner-chemistry+ccl_nospam==kressworks.com__ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com__ccl.net] On Behalf Of yang guo guoyang0123-*-gmail.com Sent: Thursday, January 20, 2011 10:10 PM To: Kress, Jim Subject: CCL:G: lanl2dz basis set: GAMESS vs G09 As far as I know, it is very common that the basis set with the same name in G09 and Gamess are different. Even the STO-3G basis set of Mg atom is different. You can use the key word 'Punch' in Gaussian to generate Gamess input file, if you want get the same result. And this website may give you some help: https://bse.pnl.gov/bse/portal 2011/1/21 Cheri Ann McFerrin cmcfer1..lsu.edu Sent to CCL by: "Cheri Ann McFerrin" [cmcfer1{:}lsu.edu ] Hi Everyone: The Lanl2dz basis for Copper at the EMSL basis set exchange (pnl.gov ) in GAMESS-US format versus the Lanl2dz basis for Copper using G09 are different. I am copying the coefficients & exponents here for convenience, separated by asterisks. Can anyone tell me why the Lanl2dz basis is not consistent with respect to GAMESS & G09? We are getting different equilibrium geometries and eneriges as a result. Thank you!! Dr. Cheri McFerrin, LSU Dept of Chemistry, Baton Rouge, LA USA **************************************************************************** ******* ! LANL2DZ ECP EMSL Basis Set Exchange Library 1/20/11 10:05 AM ! Elements References ! -------- ---------- ! H - Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Electronic Structure ! Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRESS (1977) ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). $DATA COPPER S 3 1 8.1760000 -0.4210260 2 2.5680000 0.7385924 3 0.9587000 0.5525692 S 4 1 8.1760000 0.1787665 2 2.5680000 -0.3592273 3 0.9587000 -0.4704825 4 0.1153000 1.0807407 S 1 1 0.0396000 1.0000000 P 3 1 25.6300000 -0.0489173 2 3.1660000 0.6272854 3 1.0230000 0.4716188 P 1 1 0.0860000 1.0000000 P 1 1 0.0240000 1.0000000 D 4 1 41.3400000 0.0465424 2 11.4200000 0.2227824 3 3.8390000 0.4539059 4 1.2300000 0.5314769 D 1 1 0.3102000 1.0000000 $END ! Elements References ! -------- ---------- ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). $ECP CU-ECP GEN 10 2 3 ----- d potential ----- -10.0000000 1 511.9951763 -72.5548282 2 93.2801074 -12.7450231 2 23.2206669 4 ----- s-d potential ----- 3.0000000 0 173.1180854 23.8351825 1 185.2419886 473.8930488 2 73.1517847 157.6345823 2 14.6884157 4 ----- p-d potential ----- 5.0000000 0 100.7191369 6.4990936 1 130.8345665 351.4605395 2 53.8683720 85.5016036 2 14.0989469 $END *********************from G09 output after using lanl2dz 6d********************************* S 3 1.00 0.000000000000 0.2568000000D+01 -0.4632439327D-01 0.9587000000D+00 -0.2394893745D+00 0.1153000000D+00 0.1097356778D+01 S 3 1.00 0.000000000000 0.8176000000D+01 -0.4210259893D+00 0.2568000000D+01 0.7385923813D+00 0.9587000000D+00 0.5525691860D+00 S 1 1.00 0.000000000000 0.3960000000D-01 0.1000000000D+01 P 3 1.00 0.000000000000 0.2563000000D+02 -0.4891730019D-01 0.3166000000D+01 0.6272854025D+00 0.1023000000D+01 0.4716188019D+00 P 1 1.00 0.000000000000 0.8600000000D-01 0.1000000000D+01 P 1 1.00 0.000000000000 0.2400000000D-01 0.1000000000D+01 D 4 1.00 0.000000000000 0.4134000000D+02 0.4654240160D-01 0.1142000000D+02 0.2227824077D+00 0.3839000000D+01 0.4539059156D+00 0.1230000000D+01 0.5314769183D+00 D 1 1.00 0.000000000000 0.3102000000D+00 0.1000000000D+01 **************************************************************

So, your claim is that Gaussian has unilaterally redefined the basis = sets for many atoms but retained their common = name?

 

That makes no sense.

 

Jim Kress

 

From:= = owner-chemistry+ccl_nospam=3D=3Dkressworks.com__ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com__ccl.net] On = Behalf Of yang guo guoyang0123-*-gmail.com
Sent: Thursday, = January 20, 2011 10:10 PM
To: Kress, Jim =
Subject: CCL:G: lanl2dz basis set: GAMESS vs = G09

 

As far as I know, it is very common that = the basis set with the same name in G09 and Gamess are = different. Even the STO-3G basis set of Mg atom is = different.  You can use the key word 'Punch' in Gaussian to = generate Gamess input file, if you want get the same result. And this = website may give you some help: https://bse.pnl.gov/bse/portal

2011/1/21 Cheri Ann = McFerrin cmcfer1..lsu.edu <owner-chemistry_+_ccl.net&g= t;


Sent to CCL by: "Cheri Ann = McFerrin" [cmcfer1{:}lsu.edu]
Hi Everyone:

The Lanl2dz basis = for Copper at the EMSL basis set exchange (pnl.gov) in GAMESS-US format versus
the Lanl2dz = basis for Copper using G09 are different.  I am copying the = coefficients & exponents
here for convenience, separated by = asterisks.  Can anyone tell me why the Lanl2dz basis is = not
consistent with respect to GAMESS & G09?  We are getting = different equilibrium geometries and
eneriges as a = result.

Thank you!!

Dr. Cheri McFerrin, LSU Dept of = Chemistry, Baton Rouge, LA = USA
******************************************************************= *****************
!  LANL2DZ ECP  EMSL  Basis Set = Exchange Library   1/20/11 10:05 AM
! Elements     =                     =     References
! --------         =                     = ----------
! H  - Ne: T. H. Dunning Jr. and P. J. Hay, in = Methods of Electronic Structure
! Theory, Vol. 2, H. F. Schaefer III, = ed., PLENUM PRESS (1977)
! Na - Hg: P. J. Hay and W. R. Wadt, J. = Chem. Phys. 82, 270 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. = Phys. 82, 284 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, = 299 (1985).
$DATA
COPPER
S   3
 1     =  8.1760000             = -0.4210260
 2      2.5680000       =        0.7385924
 3     =  0.9587000             =  0.5525692
S   4
 1      8.1760000 =              0.1787665
 2 =      2.5680000             = -0.3592273
 3      0.9587000       =       -0.4704825
 4      0.1153000 =              1.0807407
S   = 1
 1      0.0396000         =      1.0000000
P   3
 1     = 25.6300000             = -0.0489173
 2      3.1660000       =        0.6272854
 3     =  1.0230000             =  0.4716188
P   1
 1      0.0860000 =              1.0000000
P   = 1
 1      0.0240000         =      1.0000000
D   4
 1     = 41.3400000             =  0.0465424
 2     11.4200000       =        0.2227824
 3     =  3.8390000             =  0.4539059
 4      1.2300000     =          0.5314769
D   1
 1 =      0.3102000             =  1.0000000
$END
! Elements           =                   = References
! --------             =                 ----------
! = Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! =          P. J. Hay and W. R. Wadt, J. Chem. = Phys. 82, 284 (1985).
!          P. J. Hay = and W. R. Wadt, J. Chem. Phys. 82, 299 = (1985).
 $ECP
 CU-ECP GEN     10     = 2
 3      ----- d potential     = -----
   -10.0000000        1   =  511.9951763
   -72.5548282       =  2     93.2801074
   -12.7450231   =      2     23.2206669
 4     =  ----- s-d potential     -----
    =  3.0000000        0   =  173.1180854
    23.8351825       =  1    185.2419886
   473.8930488   =      2     73.1517847
  =  157.6345823        2     = 14.6884157
 4      ----- p-d potential   =   -----
     5.0000000       =  0    100.7191369
     6.4990936   =      1    130.8345665
  =  351.4605395        2     = 53.8683720
    85.5016036        2 =     14.0989469
 $END
*********************from G09 = output after using lanl2dz = 6d*********************************
 S   3 1.00   =     0.000000000000
     0.2568000000D+01 = -0.4632439327D-01
     0.9587000000D+00 = -0.2394893745D+00
     0.1153000000D+00 =  0.1097356778D+01
 S   3 1.00       = 0.000000000000
     0.8176000000D+01 = -0.4210259893D+00
     0.2568000000D+01 =  0.7385923813D+00
     0.9587000000D+00 =  0.5525691860D+00
 S   1 1.00       = 0.000000000000
     0.3960000000D-01 =  0.1000000000D+01
 P   3 1.00       = 0.000000000000
     0.2563000000D+02 = -0.4891730019D-01
     0.3166000000D+01 =  0.6272854025D+00
     0.1023000000D+01 =  0.4716188019D+00
 P   1 1.00       = 0.000000000000
     0.8600000000D-01 =  0.1000000000D+01
 P   1 1.00       = 0.000000000000
     0.2400000000D-01 =  0.1000000000D+01
 D   4 1.00       = 0.000000000000
     0.4134000000D+02 =  0.4654240160D-01
     0.1142000000D+02 =  0.2227824077D+00
     0.3839000000D+01 =  0.4539059156D+00
     0.1230000000D+01 =  0.5314769183D+00
 D   1 1.00       = 0.000000000000
     0.3102000000D+00 =  0.1000000000D+01
***********************************************= ***************



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------=_NextPart_000_000D_01CBB95F.42A1C200-- From owner-chemistry@ccl.net Fri Jan 21 15:36:01 2011 From: "WU Yanbin wuyb02^gmail.com" To: CCL Subject: CCL: Zero-point energy calculations between two species Message-Id: <-43725-110121132025-8011-xOhILuT4mDVbU8zQKD0/gA|*|server.ccl.net> X-Original-From: WU Yanbin Content-Type: multipart/alternative; boundary=0016367fae6fff6662049a5f4cba Date: Fri, 21 Jan 2011 12:20:11 -0600 MIME-Version: 1.0 Sent to CCL by: WU Yanbin [wuyb02!A!gmail.com] --0016367fae6fff6662049a5f4cba Content-Type: text/plain; charset=ISO-8859-1 Dear all, I'm using MP2/aug-cc-pVDZ to compute the interaction energy between two species A and B. The electronic interaction energy was corrected for basis set superposition error by counterpoise method. In order to compare with experimental interaction energy, the zero point energy (ZPE) needs to be added to the electronic interaction energy. My question is: Should be delta(ZPE) be computed by ZPE(A+B)-ZPE(A_B)-ZPE(B_A), or just ZPE(A+B)-Z(A)-Z(B)? ZPE(A+B) is the zero point energy for the A+B dimer. ZPE(A_B) is the zero point energy for A, with B as ghost atom. Similar for ZPE(B_A). ZPE(A) is the zero point energy for A monomer. Similar for ZPE(B_A). Do let me know if the question is not made clear. Thank you. Best, Yanbin --0016367fae6fff6662049a5f4cba Content-Type: text/html; charset=ISO-8859-1 Dear all,

I'm using MP2/aug-cc-pVDZ to compute the interaction energy between two species A and B.
The electronic interaction energy was corrected for basis set superposition error by counterpoise method.

In order to compare with experimental interaction energy, the zero point energy (ZPE) needs to be added to the electronic interaction energy.

My question is:
Should be delta(ZPE) be computed by ZPE(A+B)-ZPE(A_B)-ZPE(B_A), or just ZPE(A+B)-Z(A)-Z(B)?
ZPE(A+B) is the zero point energy for the A+B dimer.
ZPE(A_B) is the zero point energy for A, with B as ghost atom. Similar for ZPE(B_A).
ZPE(A) is the zero point energy for A monomer. Similar for ZPE(B_A).

Do let me know if the question is not made clear.

Thank you.

Best,
Yanbin
--0016367fae6fff6662049a5f4cba-- From owner-chemistry@ccl.net Fri Jan 21 16:59:00 2011 From: "Jason DAcchioli jdacchio * gmail.com" To: CCL Subject: CCL:G: Gaussian on Centos? Message-Id: <-43726-110121125453-15710-cpWdPYH63L+A084ENr3Iow- -server.ccl.net> X-Original-From: Jason DAcchioli Content-Type: multipart/alternative; boundary=0016362851b6cf4ef8049a5eef27 Date: Fri, 21 Jan 2011 11:54:07 -0600 MIME-Version: 1.0 Sent to CCL by: Jason DAcchioli [jdacchio|gmail.com] --0016362851b6cf4ef8049a5eef27 Content-Type: text/plain; charset=ISO-8859-1 Hi Jason, I did try. Honest, I did, but with no luck (I took a look at the link you sent a few months ago, but again, no dice). If anyone else out there has a good recipe, please let me know! Thanks again for the info. Be well, Jason On Thu, Jan 20, 2011 at 5:06 PM, Jason Swails swails%qtp.ufl.edu < owner-chemistry^^^ccl.net> wrote: > > > On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com < > owner-chemistry(_)ccl.net > wrote: > >> Hi Daniel, >> >> Both Gaussian and Gaussview will run on CentOS; I've got it working on an >> Altix XE310 in my lab. A word of warning, though; if you get Gaussview, it >> will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other >> open-source Linux flavor (easily, at least). > > > ooh! A challenge! Were it not for the hefty price tag I'd give it a go. > An ubuntu thread that may be helpful: > http://ubuntuforums.org/showthread.php?t=634578 > > In any case, Linux is Linux, so I can't imagine it's completely > incompatible with other flavors. It may be necessary to install additional > packages with the proper library versions. > > As a side-note, SUSE 10 is listed as a supported platform if an additional > package is installed. > > All the best, > Jason > > >> >> Be well, >> >> Jason >> >> Jason S. D'Acchioli >> Assistant Professor of Chemistry >> University of Wisconsin-Stevens Point >> >> On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu < >> owner-chemistry],[ccl.net> wrote: >> >>> >>> Sent to CCL by: Daniel Strahs [dstrahs**pace.edu] >>> Hello colleagues: >>> >>> Has any one had any experience installing Gaussian for Linux/Red Hat >>> Enterprise on the Centos OS? The binary compatibility with RedHat >>> interests us. >>> >>> Thanks for any responses! >>> >>> -- >>> Daniel B. Strahs >>> Associate Professor >>> Biology and Health Sciences Department >>> Pace University, New York>>> E-mail to subscribers: CHEMISTRY],[ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use>>> >>> >>> >> > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > --0016362851b6cf4ef8049a5eef27 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Jason,

I did try. Honest, I did, but with no luck (I took a look = at the link you sent a few months ago, but again, no dice). If anyone else = out there has a good recipe, please let me know! Thanks again for the info.=

Be well,

Jason

On Thu, Jan 20,= 2011 at 5:06 PM, Jason Swails swails%qtp.uf= l.edu <= owner-chemistry^^^ccl.net> wrote:


On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com <owner-chemistry(_)ccl.net> wrote:
Hi Daniel,

Both Gaussian and Gaussvie= w will run on CentOS; I've got it working on an Altix XE310 in my lab. = A word of warning, though; if you get Gaussview, it will only run on CentOS= or Redhat. It doesn't run on Ubuntu, or any other open-source Linux fl= avor (easily, at least).

ooh! A challenge! =A0Were it not for the hefty pr= ice tag I'd give it a go. =A0An ubuntu thread that may be helpful: =A0<= a href=3D"http://ubuntuforums.org/showthread.php?t=3D634578" target=3D"_bla= nk">http://ubuntuforums.org/showthread.php?t=3D634578

In any case, Linux is Linux, so I can't imagine it&= #39;s completely incompatible with other flavors. =A0It may be necessary to= install additional packages with the proper library versions.

As a side-note, SUSE 10 is listed as a supported platform if= an additional package is installed.

All the best,=
Jason



Be well,

Jason

Jason S. D'Acchioli
Assistant Profe= ssor of Chemistry
University of Wisconsin-Stevens Point

On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|= pace.edu <owner-= chemistry],[ccl.net> wrote:

Sent to CCL by: Daniel Strahs [dstrahs**pace.edu]
Hello colleagues:

Has any one had any experience installing Gaussian for Linux/Red Hat
Enterprise on the Centos OS? The binary compatibility with RedHat
interests us.

Thanks for any responses!

--
Daniel B. Strahs
Associate Professor
Biology and Health Sciences Department
Pace University, New York



-=3D This is automatically added to each message by the mailing script =3D-
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--
Jason M. Swails
Quantum Theory Project,
University of Fl= orida
Ph.D. Graduate Student
352-392-4032

--0016362851b6cf4ef8049a5eef27-- From owner-chemistry@ccl.net Fri Jan 21 19:53:00 2011 From: "Jason Swails swails||qtp.ufl.edu" To: CCL Subject: CCL:G: Gaussian on Centos? Message-Id: <-43727-110121190404-21220-1UidyRA/sBPQoQmJHSzGeA!=!server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=00163646d73ae6418f049a641916 Date: Fri, 21 Jan 2011 19:03:48 -0500 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails__qtp.ufl.edu] --00163646d73ae6418f049a641916 Content-Type: text/plain; charset=ISO-8859-1 Hi (myself? :), I'm sure you tried, and I'm by no means implying it would be easy (or that I'd be able to do it when all's said and done). I'd certainly like to try. I'll dig around here and see if we don't have some kind of site license that will let me attempt it. Without it, Gaussian and GaussView are much to expensive to expect an individual to swallow the cost (especially for a graduate student). I merely remarked that it must be POSSIBLE to install GaussView on any Linux flavor, since at the end of the day Linux is Linux. However, all flavors of Linux are different, and different groups decide that different components are "essential", so the likelihood that it'll work out-of-the-box on all/most distributions is slim-to-none. Not having access to the source code and being able to compile it on-site means that we have to pick and guess about the ones that GaussView was linked to at the time it was built, or any of the other dependencies that it may have. Furthermore, Gaussian is faced with one of 2 options: 1) Work to make GaussView as compatible as possible with as many platforms as possible. 2) Make it work well with 1 platform and make that a prerequisite. Based on the relative difficulty of the two, you can hardly be surprised they went with the latter. All the best, Jason On Fri, Jan 21, 2011 at 12:54 PM, Jason DAcchioli jdacchio * gmail.com < owner-chemistry.:.ccl.net> wrote: > Hi Jason, > > I did try. Honest, I did, but with no luck (I took a look at the link you > sent a few months ago, but again, no dice). If anyone else out there has a > good recipe, please let me know! Thanks again for the info. > > Be well, > > Jason > > On Thu, Jan 20, 2011 at 5:06 PM, Jason Swails swails%qtp.ufl.edu < > owner-chemistry{:}ccl.net > wrote: > >> >> >> On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com < >> owner-chemistry(_)ccl.net > wrote: >> >>> Hi Daniel, >>> >>> Both Gaussian and Gaussview will run on CentOS; I've got it working on an >>> Altix XE310 in my lab. A word of warning, though; if you get Gaussview, it >>> will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other >>> open-source Linux flavor (easily, at least). >> >> >> ooh! A challenge! Were it not for the hefty price tag I'd give it a go. >> An ubuntu thread that may be helpful: >> http://ubuntuforums.org/showthread.php?t=634578 >> >> In any case, Linux is Linux, so I can't imagine it's completely >> incompatible with other flavors. It may be necessary to install additional >> packages with the proper library versions. >> >> As a side-note, SUSE 10 is listed as a supported platform if an additional >> package is installed. >> >> All the best, >> Jason >> >> >>> >>> Be well, >>> >>> Jason >>> >>> Jason S. D'Acchioli >>> Assistant Professor of Chemistry >>> University of Wisconsin-Stevens Point >>> >>> On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu < >>> owner-chemistry],[ccl.net> wrote: >>> >>>> >>>> Sent to CCL by: Daniel Strahs [dstrahs**pace.edu] >>>> Hello colleagues: >>>> >>>> Has any one had any experience installing Gaussian for Linux/Red Hat >>>> Enterprise on the Centos OS? The binary compatibility with RedHat >>>> interests us. >>>> >>>> Thanks for any responses! >>>> >>>> -- >>>> Daniel B. Strahs >>>> Associate Professor >>>> Biology and Health Sciences Department >>>> Pace University, New York>>>> E-mail to subscribers: CHEMISTRY],[ccl.net or use:>>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use>>>> >>>> >>>> >>> >> >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Graduate Student >> 352-392-4032 >> > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --00163646d73ae6418f049a641916 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi (myself? :),

I'm sure you tried, and I'm by no means impl= ying it would be easy (or that I'd be able to do it when all's said= and done).=A0 I'd certainly like to try.=A0 I'll dig around here a= nd see if we don't have some kind of site license that will let me atte= mpt it.=A0 Without it, Gaussian and GaussView are much to expensive to expe= ct an individual to swallow the cost (especially for a graduate student).
I merely remarked that it must be POSSIBLE to install GaussView on any = Linux flavor, since at the end of the day Linux is Linux.=A0 However, all f= lavors of Linux are different, and different groups decide that different c= omponents are "essential", so the likelihood that it'll work = out-of-the-box on all/most distributions is slim-to-none. Not having access= to the source code and being able to compile it on-site means that we have= to pick and guess about the ones that GaussView was linked to at the time = it was built, or any of the other dependencies that it may have.

Furthermore, Gaussian is faced with one of 2 options: 1) Work to make G= aussView as compatible as possible with as many platforms as possible. 2) M= ake it work well with 1 platform and make that a prerequisite.=A0 Based on = the relative difficulty of the two, you can hardly be surprised they went w= ith the latter.

All the best,
Jason

On Fri, Jan 21= , 2011 at 12:54 PM, Jason DAcchioli jdacchio * gmail.com <owner-chemistry.:.ccl.net> wrote:
Hi Jason,

= I did try. Honest, I did, but with no luck (I took a look at the link you s= ent a few months ago, but again, no dice). If anyone else out there has a g= ood recipe, please let me know! Thanks again for the info.

Be well,

Jason

On Thu, Jan 20,= 2011 at 5:06 PM, Jason Swails swails%qtp.ufl.edu <owner-chemistry{:}ccl.net&g= t; wrote:


On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.co= m <owner-chemistry(_)ccl.net> wrote:
Hi Daniel,
Both Gaussian and Gaussview will run on CentOS; I've got it working on= an Altix XE310 in my lab. A word of warning, though; if you get Gaussview,= it will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any= other open-source Linux flavor (easily, at least).

ooh! A challenge! =A0Were it not for the hefty pr= ice tag I'd give it a go. =A0An ubuntu thread that may be helpful: =A0<= a href=3D"http://ubuntuforums.org/showthread.php?t=3D634578" target=3D"_bla= nk">http://ubuntuforums.org/showthread.php?t=3D634578

In any case, Linux is Linux, so I can't imagine it&= #39;s completely incompatible with other flavors. =A0It may be necessary to= install additional packages with the proper library versions.

As a side-note, SUSE 10 is listed as a supported platform if= an additional package is installed.

All the best,=
Jason



Be well,

Jason

Jason S. D'Acchioli
Assistant Profe= ssor of Chemistry
University of Wisconsin-Stevens Point

On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|= pace.edu <owner-= chemistry],[ccl.net> wrote:

Sent to CCL by: Daniel Strahs [dstrahs**pace.edu]
Hello colleagues:

Has any one had any experience installing Gaussian for Linux/Red Hat
Enterprise on the Centos OS? The binary compatibility with RedHat
interests us.

Thanks for any responses!

--
Daniel B. Strahs
Associate Professor
Biology and Health Sciences Department
Pace University, New York



-=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

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/






--
Jason M. Swails
Quantum Theory Project,
University of Fl= orida
Ph.D. Graduate Student
352-392-4032




--
Jason M. Swails
Quan= tum Theory Project,
University of Florida
Ph.D. Graduate Student
3= 52-392-4032
--00163646d73ae6418f049a641916-- From owner-chemistry@ccl.net Fri Jan 21 20:28:00 2011 From: "Igor Filippov Contr igorf_+_helix.nih.gov" To: CCL Subject: CCL:G: Gaussian on Centos? Message-Id: <-43728-110121174534-15355-pjuh/hyP8WupL6/v5iqeiA*|*server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 21 Jan 2011 17:45:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf/a\helix.nih.gov] We run Gaussian 03 and GausView 4.1 on CentOs 4 without any problems. All three are a bit old but working fine for our purposes. Personally I'm somewhat skeptical about the claims that Gaussian speed depends on the flavor of Linux (i.e. OpenSuse vs. CentOs), my guess would be the culprit was properly optimized ATLAS libraries or a similar issue. While personally (again) I don't like Ubuntu - too much fancy GUI frontend to be productive, I'm not sure what the previous poster meant by "It doesn't run on Ubuntu, or any other open-source Linux flavor" - as versus, say, closed-source Linux? Is there any other kind of Linux but open source? My 2 cents, Igor On Fri, 2011-01-21 at 12:54 -0500, Jason DAcchioli jdacchio * gmail.com wrote: > Hi Jason, > > I did try. Honest, I did, but with no luck (I took a look at the link > you sent a few months ago, but again, no dice). If anyone else out > there has a good recipe, please let me know! Thanks again for the > info. > > Be well, > > Jason > > On Thu, Jan 20, 2011 at 5:06 PM, Jason Swails swails%qtp.ufl.edu > wrote: > > > On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli > jdacchio---gmail.com wrote: > Hi Daniel, > > Both Gaussian and Gaussview will run on CentOS; I've > got it working on an Altix XE310 in my lab. A word of > warning, though; if you get Gaussview, it will only > run on CentOS or Redhat. It doesn't run on Ubuntu, or > any other open-source Linux flavor (easily, at least). > > > ooh! A challenge! Were it not for the hefty price tag I'd > give it a go. An ubuntu thread that may be helpful: > http://ubuntuforums.org/showthread.php?t=634578 > > > In any case, Linux is Linux, so I can't imagine it's > completely incompatible with other flavors. It may be > necessary to install additional packages with the proper > library versions. > > > As a side-note, SUSE 10 is listed as a supported platform if > an additional package is installed. > > > All the best, > Jason > > > > > > Be well, > > Jason > > Jason S. D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > > On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs > dstrahs|pace.edu wrote: > > Sent to CCL by: Daniel Strahs > [dstrahs**pace.edu] > Hello colleagues: > > Has any one had any experience installing > Gaussian for Linux/Red Hat > Enterprise on the Centos OS? The binary > compatibility with RedHat > interests us. > > Thanks for any responses! > > -- > Daniel B. Strahs > Associate Professor > Biology and Health Sciences Department > Pace University, New York > > > > -= This is automatically added to each message > by the mailing script =- > E-mail to subscribers: CHEMISTRY],[ccl.net or > use:> > E-mail to administrators: > CHEMISTRY-REQUEST],[ccl.net or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > From owner-chemistry@ccl.net Fri Jan 21 21:03:00 2011 From: "Arun Sharma aksharma(a)usc.edu" To: CCL Subject: CCL: Find a protein with specified repeat patterns Message-Id: <-43729-110121180837-18237-ALyIErVk+R1PnUcRnOFAgw/./server.ccl.net> X-Original-From: "Arun Sharma" Date: Fri, 21 Jan 2011 18:08:36 -0500 Sent to CCL by: "Arun Sharma" [aksharma(-)usc.edu] Hello List, I want to find proteins which contain specified repeat patterns like Ala-Ala-Ala and specify how many such patterns should be present in the structure. Does anybody know if there are any websites or programs which allow discovery of proteins in this fashion from the PDB database. I've looked at SCOP, CATH, ProtoNet, etc. but none of them does exactly what I need. Thank you, Arun.