From owner-chemistry@ccl.net Wed Mar 18 01:50:00 2015 From: "Abhijit Dutta adutta.chem89(!)gmail.com" To: CCL Subject: CCL: problem of solving binding energy calculation of metal cluster Message-Id: <-51132-150318012629-1353-vNSa7DCgudEa2QpaN1J7LQ,+,server.ccl.net> X-Original-From: Abhijit Dutta Content-Type: multipart/alternative; boundary=001a114031a0a1d1220511895208 Date: Tue, 17 Mar 2015 22:26:18 -0700 MIME-Version: 1.0 Sent to CCL by: Abhijit Dutta [adutta.chem89|gmail.com] --001a114031a0a1d1220511895208 Content-Type: text/plain; charset=UTF-8 sir, Actually i am doing some work on transition metal cluster, but i am confused in determining the binding energy of respective metal cluster. Actually i am doing my calculation in DMOL3 , in the output file i found the term binding energy, but when i calculating the binding energy with the formula the value is different from the value obtained from output file.so please suggest me to solve it. --001a114031a0a1d1220511895208 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
sir,
Actually i am doing some work on transition metal= cluster, but i am confused in determining the binding energy of respective= metal cluster. Actually i am doing my calculation in DMOL3 , in the output= file i found the term binding energy, but when i calculating the binding e= nergy with the formula the value is different from the value obtained from = output file.so please suggest me to solve it.=C2=A0
--001a114031a0a1d1220511895208-- From owner-chemistry@ccl.net Wed Mar 18 05:05:01 2015 From: "Sergio Manzetti sergio.manzetti|,|outlook.com" To: CCL Subject: CCL: Gaussian command and second derivatives Message-Id: <-51133-150318050403-17073-ojZZq22owTUzIYhYAgbHYQ,+,server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 05:04:01 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] Dear all, I am not sure where in the following G09 command the second order derivatives are issued (not actually looking to use them at all): !QCISD(FULL,Conver=16,MaxCyc=1400)/genECP %mem=9686MB %chk=R.chk %nprocshared=4 #P QCISD(FULL,Conver=16,MaxCyc=1400)/genECP # Opt MaxDisk=50GB # Freq(VCD,Raman,Numerical) pop=NBOREAD # Gfinput IOP(6/7=3) Pop=full Density Test # Units(Ang,Deg) Which part of this command line issues the second order derivatives? Thanks From owner-chemistry@ccl.net Wed Mar 18 07:11:01 2015 From: "Brian Skinn bskinn#,#alum.mit.edu" To: CCL Subject: CCL:G: Gaussian command and second derivatives Message-Id: <-51134-150318070049-11675-RCJJW6YIH2T2Zco3kzQUeA%x%server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7b874664949e0505118dfe22 Date: Wed, 18 Mar 2015 07:00:22 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn!=!alum.mit.edu] --047d7b874664949e0505118dfe22 Content-Type: text/plain; charset=UTF-8 Sergio- The following line (at minimum) is one which requests the second derivatives: # Freq(VCD,Raman,Numerical) pop=NBOREAD Vibrational frequency calculations are impossible without the Hessian matrix of nuclear displacements, whether numerical or analytical. I don't know Gaussian's IOp codes by heart, so I have no idea what role that might be playing. -Brian On Wed, Mar 18, 2015 at 5:04 AM, Sergio Manzetti sergio.manzetti|,| outlook.com wrote: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] > Dear all, I am not sure where in the following G09 command the second > order derivatives are issued (not actually looking to use them at all): > > !QCISD(FULL,Conver=16,MaxCyc=1400)/genECP > %mem=9686MB > %chk=R.chk > %nprocshared=4 > #P QCISD(FULL,Conver=16,MaxCyc=1400)/genECP > # Opt MaxDisk=50GB > # Freq(VCD,Raman,Numerical) pop=NBOREAD > # Gfinput IOP(6/7=3) Pop=full Density Test > # Units(Ang,Deg) > > Which part of this command line issues the second order derivatives? > > Thanks> > > --047d7b874664949e0505118dfe22 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Sergio-

The following line (at mi= nimum) is one which requests the second derivatives:

# Freq(VCD,Raman,Numerical) pop= =3DNBOREAD
Vibrationa= l frequency calculations are impossible without the Hessian matrix of nucle= ar displacements, whether numerical or analytical.

I don't know Gaussian's IOp codes by = heart, so I have no idea what role that might be playing.
=
-Brian

<= br>

On Wed, Mar 18, 2015 at 5:04 AM, Sergio Manzetti sergio.manzetti|,|outlook.com <owner-chemistry(a)ccl.net<= /a>> wrote:

Sent to CCL by: "Sergio=C2=A0 Manzetti" [sergio.manzetti#outlook.com]
Dear all, I am not sure where in the following G09 command the second order= derivatives are issued (not actually looking to use them at all):

!QCISD(FULL,Conver=3D16,MaxCyc=3D1400)/genECP
%mem=3D9686MB
%chk=3DR.chk
%nprocshared=3D4
#P QCISD(FULL,Conver=3D16,MaxCyc=3D1400)/genECP
# Opt MaxDisk=3D50GB
# Freq(VCD,Raman,Numerical) pop=3DNBOREAD
# Gfinput IOP(6/7=3D3)=C2=A0 Pop=3Dfull=C2=A0 Density=C2=A0 Test
# Units(Ang,Deg)

Which part of this command line issues the second order derivatives?

Thanks



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--047d7b874664949e0505118dfe22-- From owner-chemistry@ccl.net Wed Mar 18 07:53:01 2015 From: "Sergio Manzetti sergio.manzetti*outlook.com" To: CCL Subject: CCL: Gaussian Job Message-Id: <-51135-150318075118-28515-760VDPvCrfFAgaJLQTvnFg]-[server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 07:51:16 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)? Thanks From owner-chemistry@ccl.net Wed Mar 18 08:52:01 2015 From: "Susi Lehtola susi.lehtola|a|alumni.helsinki.fi" To: CCL Subject: CCL: The importance of analytic second derivatives Message-Id: <-51136-150318020148-7469-ESZT2ZcAMNC+6f6mVT3d/w]![server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 17 Mar 2015 23:01:36 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola]*[alumni.helsinki.fi] On 03/17/2015 04:44 PM, Víctor Luaña Cabal victor*o*fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor=fluor.quimica.uniovi.es] > On Tue, Mar 17, 2015 at 09:40:39AM -0700, Susi Lehtola susi.lehtola:_:alumni.helsinki.fi wrote: >> Examples of methods that implement derivatives of the energy with >> respect to the orbitals are multi-configurational self-consistent field >> theory, and orbital-optimized theories such as orbital-optimized MP2 and >> orbital-optimized doubles (OD). > > Thanks for the correction. I didn't thought on these before writing. Of course I left out the most obvious solution. Namely, the orbitals are optimized in any self-consistent field method. That's what determines your self-consistent field solution! -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola:-:alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Mar 18 09:27:00 2015 From: "Sergio Manzetti sergio.manzetti]~[outlook.com" To: CCL Subject: CCL:G: Pseudopotentials in GAMESS Message-Id: <-51137-150318081606-9990-GNMRUcyRUaIRAk0WnAy9kw++server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 08:16:05 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti],[outlook.com] Hi, I am not sure on using pseudopotentials in GAMESS. In gaussian they need an orbital section and a projection section. However, for GAMESS I only found: http://vallico.net/casinoqmc/pplib/ The Quantum Monte Carlo external basis sets include seemingly only one section: DF Pseudopotential fit - GAMESS format ====================================== Element : Mo When : 18 Nov 05 $ECP Mo-DFECP GEN 36 2 6 ..... Vd ..... 6.00000000 1 2.31511157 -1.62200777 2 0.59540433 -11.97198740 2 1.75455232 -4.41067762 2 3.16192178 5.41067762 2 6.63825290 13.89066941 3 2.38835093 6 ..... Vs-Vd ..... -2.56521584 2 0.63714525 12.10720714 2 0.94172614 79.64058274 2 1.11391926 -239.85938008 2 1.56395508 457.40941134 2 2.14827029 -296.18991197 2 2.38357271 6 ..... Vp-Vd ..... -286.12116945 2 0.44852876 294.66712698 2 0.87888131 283.20086315 2 0.44812492 -310.72400818 2 0.93296054 90.98284588 2 2.09387209 -62.45863629 2 2.53233872 $END this looks rather poor for an external basis set with projections? From owner-chemistry@ccl.net Wed Mar 18 10:35:01 2015 From: "Mark Zottola mzottola*o*gmail.com" To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51138-150318103302-7791-QxTy9zUxWtebc9MxKc3/wA.@.server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=e89a8ffbae418b2802051190f5e7 Date: Wed, 18 Mar 2015 21:32:55 +0700 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola^^^gmail.com] --e89a8ffbae418b2802051190f5e7 Content-Type: text/plain; charset=UTF-8 Gaussian has one of the best optimizers for QM. Before trashing G09, make sure your structure is indeed correct chemically. Second, optimizing a structure at a lower level of theory and then re-optimizing at a higher level of theory often (not always) overcomes convergence issues wrt structure. Thirdly, your comments are ambiguous. Do you mean to say that the wavefunction did not converge or that there were difficulties in getting a converged wavefunction? Or do you mean the optimization did not converge? If the latter and there is not an issue with cpu time, why quit on Gaussian? If your issue is with the convergence of the wavefunction alone, then there is plenty on both the G09 web site and the CCL archives about approaches to dealing with unstable wavefunctions. If your system is pathogenic using G09 and wish to explore another program NWCHEM, a very-well parallelized QM code might be better than GAMESS. THe former is also free, assuming you have no export considerations to contend with. On Wed, Mar 18, 2015 at 6:51 PM, Sergio Manzetti sergio.manzetti*outlook.com wrote: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] > Thanks Brian. At the end of the day, G09 was not able to solve this > structure. I am trying GAMESS instead, however I cannot find an equivalent > to CASSCF method in the example section of GAMESS US. Can anyone recommend > the most accurate method to treat a very small system (Computational time > and speed is irrelevant)? > > Thanks> > > --e89a8ffbae418b2802051190f5e7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Gaussian has one of the best optimizers for QM.=C2=A0 Befo= re trashing G09, make sure your structure is indeed correct chemically.
Second, optimizing a structure at a lower level of theory a= nd then re-optimizing at a higher level of theory often (not always) overco= mes convergence issues wrt structure.

Thirdly, you= r comments are ambiguous.=C2=A0 Do you mean to say that the wavefunction di= d not converge or that there were difficulties in getting a converged wavef= unction?=C2=A0 Or do you mean the optimization did not converge?=C2=A0 If t= he latter and there is not an issue with cpu time, why quit on Gaussian?

If your issue is with the convergence of the wavefun= ction alone, then there is plenty on both the G09 web site and the CCL arch= ives about approaches to dealing with unstable wavefunctions.
If your system is pathogenic using G09 and wish to explore anot= her program NWCHEM, a very-well parallelized QM code might be better than G= AMESS.=C2=A0 THe former is also free, assuming you have no export considera= tions to contend with.

On Wed, Mar 18, 2015 at 6:51 PM, Sergio Manzetti sergio.ma= nzetti*outlook.com <= ;owner-chemist= ry###ccl.net> wrote:

Sent to CCL by: "Sergio=C2=A0 Manzetti" [sergio.manzetti__outlook.com]=
Thanks Brian. At the end of the day, G09 was not able to solve this structu= re. I am trying GAMESS instead, however I cannot find an equivalent to CASS= CF=C2=A0 method in the example section of GAMESS US. Can anyone recommend t= he most accurate method to treat a very small system (Computational time an= d speed is irrelevant)?

Thanks



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--e89a8ffbae418b2802051190f5e7-- From owner-chemistry@ccl.net Wed Mar 18 11:10:01 2015 From: "Robert Molt r.molt.chemical.physics^_^gmail.com" To: CCL Subject: CCL: Gaussian Job Message-Id: <-51139-150318103514-8683-TdA+LrDU596r+QK4aypBYA^-^server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 18 Mar 2015 10:35:05 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics.:.gmail.com] CAS, in GAMESS, is called FORS. Search for $DET in the manual. If you're intent on a very accurate wavefunction for a small molecule, I would recommend CFOUR, ACES2, Dalton, something like that. Those 3 all have coupled cluster capabilities to do CCSD, CCSDT, and CCSDTQ for CFOUR at least. They also have perturbative calculations of triples, quadruples, etc. CFOUR and ACES2 are relatively easy to use, never tried Dalton. GAMESS can do CCSD, but I believe it is a lot slower than ACES2 or CFOUR. On 3/18/15 7:51 AM, Sergio Manzetti sergio.manzetti*outlook.com wrote: > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] > Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)? > > Thanks> > -- Dr. Robert Molt Jr. r.molt.chemical.physics-$-gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Wed Mar 18 12:06:01 2015 From: "Rene Sitt Sitt-,-students.uni-marburg.de" To: CCL Subject: CCL:G: Gaussian command and second derivatives Message-Id: <-51140-150318103209-7453-+YFL24zOIgbH/PQSJeOB4A-$-server.ccl.net> X-Original-From: Rene Sitt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 18 Mar 2015 15:32:39 +0100 MIME-Version: 1.0 Sent to CCL by: Rene Sitt [Sitt{}students.uni-marburg.de] Hello, the second derivatives (of the energy, w.r.t nuclear coordinates) is needed to compute the frequencies, i.e. the 'Freq' directive in your input file. The Gaussian page has more detailed info on that: http://www.gaussian.com/g_tech/g_ur/k_freq.htm Regards, Rene Sitt On 03/18/2015 10:04 AM, Sergio Manzetti sergio.manzetti|,|outlook.com wrote: > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#outlook.com] > Dear all, I am not sure where in the following G09 command the second order derivatives are issued (not actually looking to use them at all): > > !QCISD(FULL,Conver=16,MaxCyc=1400)/genECP > %mem=9686MB > %chk=R.chk > %nprocshared=4 > #P QCISD(FULL,Conver=16,MaxCyc=1400)/genECP > # Opt MaxDisk=50GB > # Freq(VCD,Raman,Numerical) pop=NBOREAD > # Gfinput IOP(6/7=3) Pop=full Density Test > # Units(Ang,Deg) > > Which part of this command line issues the second order derivatives? > > Thanks> > From owner-chemistry@ccl.net Wed Mar 18 12:41:01 2015 From: "Robert Molt r.molt.chemical.physics:gmail.com" To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51141-150318114721-796-2k3YdQJGeRjduStzc+k4gQ{}server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------060007040900070605020105" Date: Wed, 18 Mar 2015 11:47:12 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics(~)gmail.com] This is a multi-part message in MIME format. --------------060007040900070605020105 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit S. Manzetti is not trashing Gaussian. Users trying to problem solve what's going wrong are not "trashing" a software. GAMESS and NWCHEM are both very good, well-parallelized softwares. S. Manzetti, it would be helpful if you said what your system is. If your system is "simple," maybe you do not need more accurate than Hartree-Fock for your purposes, and someone can show you how to use Gaussian or GAMESS just fine. If you need something more refined, like CCSD, people can show you how to use a good coupled cluster software like CFOUR for that. If it's a really accurate calculation you need, do CCSDT or a large CAS. On 3/18/15 10:32 AM, Mark Zottola mzottola*o*gmail.com wrote: > Gaussian has one of the best optimizers for QM. Before trashing G09, > make sure your structure is indeed correct chemically. > > Second, optimizing a structure at a lower level of theory and then > re-optimizing at a higher level of theory often (not always) overcomes > convergence issues wrt structure. > > Thirdly, your comments are ambiguous. Do you mean to say that the > wavefunction did not converge or that there were difficulties in > getting a converged wavefunction? Or do you mean the optimization did > not converge? If the latter and there is not an issue with cpu time, > why quit on Gaussian? > > If your issue is with the convergence of the wavefunction alone, then > there is plenty on both the G09 web site and the CCL archives about > approaches to dealing with unstable wavefunctions. > > If your system is pathogenic using G09 and wish to explore another > program NWCHEM, a very-well parallelized QM code might be better than > GAMESS. THe former is also free, assuming you have no export > considerations to contend with. > > On Wed, Mar 18, 2015 at 6:51 PM, Sergio Manzetti > sergio.manzetti*outlook.com > > > wrote: > > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com > ] > Thanks Brian. At the end of the day, G09 was not able to solve > this structure. I am trying GAMESS instead, however I cannot find > an equivalent to CASSCF method in the example section of GAMESS > US. Can anyone recommend the most accurate method to treat a very > small system (Computational time and speed is irrelevant)? > > Thanks > > > > -= 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/> > > -- Dr. Robert Molt Jr. r.molt.chemical.physics ~ gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 --------------060007040900070605020105 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit S. Manzetti is not trashing Gaussian.  Users trying to problem solve what's going wrong are not "trashing" a software.

GAMESS and NWCHEM are both very good, well-parallelized softwares.

S. Manzetti, it would be helpful if you said what your system is. If your system is "simple," maybe you do not need more accurate than Hartree-Fock for your purposes, and someone can show you how to use Gaussian or GAMESS just fine. If you need something more refined, like CCSD, people can show you how to use a good coupled cluster software like CFOUR for that. If it's a really accurate calculation you need, do CCSDT or a large CAS.

On 3/18/15 10:32 AM, Mark Zottola mzottola*o*gmail.com wrote:
Gaussian has one of the best optimizers for QM.  Before trashing G09, make sure your structure is indeed correct chemically.

Second, optimizing a structure at a lower level of theory and then re-optimizing at a higher level of theory often (not always) overcomes convergence issues wrt structure.

Thirdly, your comments are ambiguous.  Do you mean to say that the wavefunction did not converge or that there were difficulties in getting a converged wavefunction?  Or do you mean the optimization did not converge?  If the latter and there is not an issue with cpu time, why quit on Gaussian?

If your issue is with the convergence of the wavefunction alone, then there is plenty on both the G09 web site and the CCL archives about approaches to dealing with unstable wavefunctions.

If your system is pathogenic using G09 and wish to explore another program NWCHEM, a very-well parallelized QM code might be better than GAMESS.  THe former is also free, assuming you have no export considerations to contend with.

On Wed, Mar 18, 2015 at 6:51 PM, Sergio Manzetti sergio.manzetti*outlook.com <owner-chemistry!^!ccl.net> wrote:

Sent to CCL by: "Sergio  Manzetti" [sergio.manzetti__outlook.com]
Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF  method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)?

Thanks



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-- 
Dr. Robert Molt Jr.
r.molt.chemical.physics ~ gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
--------------060007040900070605020105-- From owner-chemistry@ccl.net Wed Mar 18 13:50:01 2015 From: "Sergio Manzetti sergio.manzetti*o*outlook.com" To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51142-150318134846-15365-TEM+QCqOohK9HgpMIymT9Q:+:server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 13:48:44 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti-x-outlook.com] Hi Mark et al. The reason for switching to GAMESS is because the output .47 file from g09 does not work with NBO6, and the g03 does not reach convergence with CI methods, OR it complaints about second analytical derivatives. CASSFC does not run at all, it stops after 27 steps without any note on what happened. Basically, trying GAMESS assures at least point 1, with NBO. part 2 may not work in GAMESS either, however it has to be tried first. The calculations should be more than quadruple excitation state if there was such a method at all! I would like quadri-deca excitation state (14 excitations) to be added to it, however, is there anything like that at all? Thanks Sergio From owner-chemistry@ccl.net Wed Mar 18 14:25:01 2015 From: "Sergio Manzetti sergio.manzetti-$-outlook.com" To: CCL Subject: CCL:G: Second analytical gradients Message-Id: <-51143-150318141201-31150-E4KLh9dbzytx+5RfeBYifw~~server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 14:11:58 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti[]outlook.com] These gradients appear as impossible to calculate even when doing calculation without frequency keyword in G03/G09 #P CASSCF(150,42,Spin,Nroot=5)/genECP # Opt # Freq pop=NBOREAD # Gfinp ut IOP(6/7=3) Density MP2 # Units(Ang,Deg) ---------------------------------------------------------------------- Warning: this job cannot use analytic gradients and so will do many energy evaluations. From owner-chemistry@ccl.net Wed Mar 18 15:45:01 2015 From: "Salter-Duke, Brian James - brian.james.duke[]gmail.com" To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51144-150318150930-19471-Jz+FL1csXsHJIY5wZvskjg|,|server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 19 Mar 2015 06:09:18 +1100 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke,gmail.com] You need SCFTYP=MCSCF in $CONTRL. GAMESS is easier to use for CASSCF than Gaussian, but forget what you learnt with Gaussian, GAMESS does it with very different contrl commands. Brian. On Wed, Mar 18, 2015 at 07:51:16AM -0400, Sergio Manzetti sergio.manzetti*outlook.com wrote: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] > Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)? > > Thanks> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke%monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Wed Mar 18 16:19:01 2015 From: "Sergio Manzetti sergio.manzetti^^outlook.com" To: CCL Subject: CCL:G: Disagremment between com and log fil ein G03 Message-Id: <-51145-150318160801-13831-IGWnYIicdIUBLUY+548zzA/a\server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 16:07:59 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti[*]outlook.com] This job was submitted: %chk=X.chk %Mem=16000MB %nprocshared=4 #P CASSCF(150,42,Spin,Nroot=5)/genECP # Opt # pop=NBOREAD # Gfinput IOP(6/7=3) Density MP2 # Units(Ang,Deg) and the log gives: Will use up to 4 processors via shared memory. ---------------------------------------------------------------------- #P CASSCF(150,42,Spin,Nroot=5)/genECP # Opt # Freq pop=NBOREAD # Gfinp ut IOP(6/7=3) Density MP2 # Units(Ang,Deg) ---------------------------------------------------------------------- Warning: this job cannot use analytic gradients and so will do many energy evaluations. No analytic first derivatives for this method. Error termination via Lnk1e in /home/apps/g03/g03-dsgroup/g03/l1.exe at Wed Mar 18 11:23:52 2015. Job cpu time: 0 days 0 hours 0 minutes 0.4 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 3 Scr= 1 The strange this is the FREQ keyword appears in the LOG file, but is not present in the COM file. Sergio From owner-chemistry@ccl.net Wed Mar 18 16:54:01 2015 From: "Sergio Manzetti sergio.manzetti:-:outlook.com" To: CCL Subject: CCL:G: Gaussian job Message-Id: <-51146-150318142136-4174-ulm9QKr0DAmt/onxWVyslQ|a|server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 18 Mar 2015 14:21:34 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti]=[outlook.com] Indeed! In fact, I have been using Gaussian at Uppsala University for 6 years, and I have always liked it. However, when trying to work out this problem With the current system, I have tested all options With G03/G09, Thanks Sergio -------------------------------------------------------------------------------- > From: owner-chemistry a ccl.net To: sergio.manzetti a gmx.com Subject: CCL:G: Gaussian Job Date: Wed, 18 Mar 2015 11:47:12 -0400 S. Manzetti is not trashing Gaussian. Users trying to problem solve what's going wrong are not "trashing" a software. GAMESS and NWCHEM are both very good, well-parallelized softwares. S. Manzetti, it would be helpful if you said what your system is. If your system is "simple," maybe you do not need more accurate than Hartree-Fock for your purposes, and someone can show you how to use Gaussian or GAMESS just fine. If you need something more refined, like CCSD, people can show you how to use a good coupled cluster software like CFOUR for that. If it's a really accurate calculation you need, do CCSDT or a large CAS. On 3/18/15 10:32 AM, Mark Zottola mzottola*o*gmail.com wrote: Gaussian has one of the best optimizers for QM. Before trashing G09, make sure your structure is indeed correct chemically. Second, optimizing a structure at a lower level of theory and then re-optimizing at a higher level of theory often (not always) overcomes convergence issues wrt structure. Thirdly, your comments are ambiguous. Do you mean to say that the wavefunction did not converge or that there were difficulties in getting a converged wavefunction? Or do you mean the optimization did not converge? If the latter and there is not an issue with cpu time, why quit on Gaussian? If your issue is with the convergence of the wavefunction alone, then there is plenty on both the G09 web site and the CCL archives about approaches to dealing with unstable wavefunctions. If your system is pathogenic using G09 and wish to explore another program NWCHEM, a very-well parallelized QM code might be better than GAMESS. THe former is also free, assuming you have no export considerations to contend with. On Wed, Mar 18, 2015 at 6:51 PM, Sergio Manzetti sergio.manzetti*outlook.com wrote: Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)? Thanks To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51147-150318162750-25158-+nyDjXPyU7jnebvzAHttkg===server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Mar 2015 16:27:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35-,-gmail.com] > The calculations should be more than quadruple excitation state if there was such a method at all! I would > like quadri-deca excitation state (14 excitations) to be added to it, however, is there anything like that at all? Yes. GAMESS and Firefly will allow you to specify the excitation level for GUGA CI and related MCSCF calculations (single, multi-state and state averaged). Using ORMAS in GAMESS should give you complete flexibility in the excitation level you desire. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com/a\ccl.net [mailto:owner-chemistry+jimkress35==gmail.com/a\ccl.net] On Behalf Of Sergio Manzetti sergio.manzetti*o*outlook.com Sent: Wednesday, March 18, 2015 1:49 PM To: Kress, Jim Subject: CCL:G: Gaussian Job Sent to CCL by: "Sergio Manzetti" [sergio.manzetti-x-outlook.com] Hi Mark et al. The reason for switching to GAMESS is because the output .47 file > from g09 does not work with NBO6, and the g03 does not reach convergence with CI methods, OR it complaints about second analytical derivatives. CASSFC does not run at all, it stops after 27 steps without any note on what happened. Basically, trying GAMESS assures at least point 1, with NBO. part 2 may not work in GAMESS either, however it has to be tried first. The calculations should be more than quadruple excitation state if there was such a method at all! I would like quadri-deca excitation state (14 excitations) to be added to it, however, is there anything like that at all? Thanks Sergiohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Mar 18 18:04:01 2015 From: "Soren Eustis soreneustis*_*gmail.com" To: CCL Subject: CCL:G: Gaussian Job Message-Id: <-51148-150318172243-15308-MER7+ERLzZINH5Lwsbh+gA(-)server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3509544154_10375695" Date: Wed, 18 Mar 2015 17:22:28 -0400 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis**gmail.com] > 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_3509544154_10375695 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Sergio, I am not a Gaussian 09 basher, by any means. It is a well developed program that is capable of running many different types of jobs efficiently. However, it does not run well in multiple nodes, and the CASSCF code is not actively developed. I would second many comments I have seen in recommending NWChem or GAMESS. They scale up well and the CASSCF portion of the codes are updated regularly. Soren On 3/18/15, 7:51 AM, "Sergio Manzetti sergio.manzetti*outlook.com" wrote: Sent to CCL by: "Sergio Manzetti" [sergio.manzetti__outlook.com] Thanks Brian. At the end of the day, G09 was not able to solve this structure. I am trying GAMESS instead, however I cannot find an equivalent to CASSCF method in the example section of GAMESS US. Can anyone recommend the most accurate method to treat a very small system (Computational time and speed is irrelevant)? Thankshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--B_3509544154_10375695 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable
Sergio,

   I am not a Gaussian 09 basher, by any means.  It is a we= ll developed program that is capable of running many different types of jobs= efficiently.  However, it does not run well in multiple nodes, and the= CASSCF code is not actively developed.  I would second many comments I= have seen in recommending NWChem or GAMESS.  They scale up well and th= e CASSCF portion of the codes are updated regularly.  

Soren

On 3/18/15, 7:51 AM, "Sergio Manzetti sergio.manzetti*outlook.com" <owner-chemistry . ccl.net> wrote:<= /div>


Sent to CCL by: "Ser= gio  Manzetti" [sergio.manzetti__outlook.com]
Thanks Bri= an. At the end of the day, G09 was not able to solve this structure. I am tr= ying GAMESS instead, however I cannot find an equivalent to CASSCF &nbs= p;method in the example section of GAMESS US. Can anyone recommend the most = accurate method to treat a very small system (Computational time and speed i= s irrelevant)?

Thanks


=

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--B_3509544154_10375695-- From owner-chemistry@ccl.net Wed Mar 18 18:39:00 2015 From: "Jim Kress jimkress35]_[gmail.com" To: CCL Subject: CCL: Force Field Benchmarks for Proteins, RNA, DNA and Lipids Message-Id: <-51149-150318163506-12230-EHOZkF2wfyetCYtqPXVb2w---server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Mar 2015 16:34:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35%gmail.com] Recently, I've been working with colleagues to develop a new force field for biochemical/ biophysical application - specifically proteins, RNA, DNA and Lipids. I've been seeking a testing/ validation suite for these type of force fields with no success. I recently noticed this publication: "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant", by Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel , J. Chem. Theory Comput., 2012, 8 (1), pp 61-74 Can anyone point me to a similar analysis of force fields for Proteins, RNA, DNA and Lipids? Thanks. Jim James Kress Ph.D., President The KressWorks Foundation C An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization "Improving Lives One Atom At A Time" TM (248) 605-8770 Learn More and Donate At: http://www.kressworks.org Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From owner-chemistry@ccl.net Wed Mar 18 19:14:01 2015 From: "Cristian Buend a-Atencio c.buendia{:}uan.edu.co" To: CCL Subject: CCL: 3rd PREFALC Computational Chemistry School of South-American and Carib Message-Id: <-51150-150318181132-23316-/RtqatJBymwQ3dQICeI8qA(0)server.ccl.net> X-Original-From: "Cristian Buend a-Atencio" Date: Wed, 18 Mar 2015 18:11:29 -0400 Sent to CCL by: "Cristian Buend a-Atencio" [c.buendia[-]uan.edu.co] 1st announcement of the 3rd PREFALC Computational Chemistry School of South-American and Caribbean Countries Dear all, We have the pleasure of announcing the 3rd PREFALC Computational Chemistry School of South-American and Caribbean Countries. This school will take place in Bogota, Colombia from June 29 to July 10, 2015. Please take note there are NO registration fees for this PREFALC edition. As in previous editions of the school we will offer a limited number of scholarships to cover for accomodation expenses. We invite all latin american students to apply for admission by filling out the application form. Please visit the event website (http://www.qcc.unal.edu.co/?mod=prefalc2015) for more information about the school and the registration process. Sincerely, Local Organizing Committee: Jorge Ali-Torres, Jrg Tatchen, Cristian Buendia, Ismael Ortiz, Andres Reyes From owner-chemistry@ccl.net Wed Mar 18 19:49:01 2015 From: "Cristian Buendia Atencio cristian.buendia+/-outlook.com" To: CCL Subject: CCL: 3rd PREFALC Computational Chemistry School of South-American and Caribbean Countries Message-Id: <-51151-150318182613-4700-Pw2N6q4E+lZQRme0ftyf7w---server.ccl.net> X-Original-From: Cristian Buendia Atencio Content-Type: multipart/alternative; boundary="_9de7f202-a26e-4074-9970-c701e6161e7a_" Date: Wed, 18 Mar 2015 17:26:06 -0500 MIME-Version: 1.0 Sent to CCL by: Cristian Buendia Atencio [cristian.buendia###outlook.com] --_9de7f202-a26e-4074-9970-c701e6161e7a_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all=2C=20 We have the pleasure of announcing the 3rd PREFALC Computational Chemistry = School of South-American and Caribbean Countries. This school will take pla= ce in Bogota=2C Colombia from June 29 to July 10=2C 2015. Please take note there are NO registration fees for this PREFALC edition. = As in previous editions of the school we will offer a limited number of sch= olarships to cover for accomodation expenses. We invite all latin american students to apply for admission by filling out= the application form. Please visit the event website (PREFALC-BOGOTA) for = more information about the school and the registration process. Sincerely=2C Local Organizing Committee:Jorge Ali-Torres=2CJ=F6rg Tatchen=2CCristian Bue= ndia=2CIsmael Ortiz=2CAndres Reyes = --_9de7f202-a26e-4074-9970-c701e6161e7a_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all=2C =3B

We have the pleasure of announcing the 3rd PREFALC Comput= ational Chemistry School of South-American and Caribbean Countries. This sc= hool will take place in Bogota=2C Colombia from June 29 to July 10=2C 2015.=


Please take note there are NO regi= stration fees for this  =3BPREFALC edition. As in previous editions of = the school we will offer a limited number of scholarships to cover for acco= modation expenses.

We invite all latin american st= udents to apply for admission by filling out the application form. Please v= isit the event website (PREFALC-BOGOTA) for more information about the scho= ol and the registration process.

Sincerely=2C

Local Organizing Committee:
Jorge Ali-Torres= =2C
J=F6rg Tatchen=2C
Cristian Buendia=2C
Ism= ael Ortiz=2C
Andres Reyes
= --_9de7f202-a26e-4074-9970-c701e6161e7a_-- From owner-chemistry@ccl.net Wed Mar 18 20:33:01 2015 From: "Youzhao Lan lyzhao(_)aliyun.com" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocalization Message-Id: <-51152-150318101753-29955-6wKlPeCehOBljORFADvong~!~server.ccl.net> X-Original-From: "Youzhao Lan" Date: Wed, 18 Mar 2015 10:17:51 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao]_[aliyun.com] Dear all, Is there a calculated parameter or quantity to characterize the degree of delocalization of pi-electron? Any help will be appreciated. Best regards. Youzhao Lan From owner-chemistry@ccl.net Wed Mar 18 21:08:00 2015 From: "Youzhao Lan lyzhao{=}aliyun.com" To: CCL Subject: CCL: How to characterize the degree of delocalization of pi-electron Message-Id: <-51153-150318195840-26570-ojZZq22owTUzIYhYAgbHYQ]~[server.ccl.net> X-Original-From: "Youzhao Lan" Date: Wed, 18 Mar 2015 19:58:38 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao _ aliyun.com] Dear all, Is there a calculated parameter or quantity to characterize the degree of delocalization of pi-electron? Any help will be appreciated. Best regards. Youzhao Lan