From owner-chemistry@ccl.net Mon Dec 12 02:03:00 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis*borealisgroup.com" To: CCL Subject: CCL: MC simulation Message-Id: <-46021-111212015226-12529-+gA8Eam0qFCSFnFgsNmH1Q:_:server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 12 Dec 2011 07:52:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis#%#borealisgroup.com] Traditionally Monte Carlo simulations are custom made since it is very difficult to have a basic code that can be used (as is) for every problem. Therefore I think you will be better off if you try to narrow down exactly what your MC code needs to do. As soon as you do this you can either try to find a readymade code or you can write one on your own. MC codes are, generally speaking, easy so it should not be too difficult as soon as you know what you want the program to do. Nevertheless since you have asked for available software have a look at this page http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling where a number of programs (commercial and not) are listed. I hope that helps Thomas Dr Thomas Gkourmpis Researcher Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com###ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com###ccl.net] On Behalf Of sofi mimi takan wafaab2*yahoo.fr Sent: Friday, December 09, 2011 6:48 PM To: Gkourmpis, Thomas Subject: CCL: MC simulation Sent to CCL by: "sofi mimi takan" [wafaab2%%yahoo.fr] Many thanks Pr. Thomas for the response. I want download a free program that runs on windows. This program whose is a general purpose molecular modeling system that performs Metropolis Monte Carlo (MC) statistical mechanics simulations. The MC simulations can be carried out for effects of solvation on relative energies of conformers, changes in free energies of solvation along reaction paths, and structures. Best regards,http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Mon Dec 12 05:12:01 2011 From: "LARA MARTINEZ FERNANDEZ lara.martinez!A!uam.es" To: CCL Subject: CCL: TD-DFT vertical spectrum vs geometry optimization Message-Id: <-46022-111212051022-2727-Mzko45kY7zYPeskfe0v3vw-#-server.ccl.net> X-Original-From: "LARA MARTINEZ FERNANDEZ" Date: Mon, 12 Dec 2011 05:10:20 -0500 Sent to CCL by: "LARA MARTINEZ FERNANDEZ" [lara.martinez_+_uam.es] Dear CCLers, We are trying to optimize the first excited triplet of a Au complex. For this, we have performed a UPBE1PBE geometry optimization. #P PBE1PBE/gen pseudo=read opt POP=FULL GFINPUT GFPRINT IOP(6/7=3) Title Card Required 0 3 .. On the optimized geometry we have performed a TD-PBE1PBE calculation. #P PBE1PBE/gen pseudo=read TD(triplets,NStates=5) POP=FULL GFINPUT GFPRINT IOP(6/7=3) scf=tight Title Card Required 0 1 .. We were expecting to obtain the same energy from the geometry optimization and from the first TD-DFT root, but these energies in fact differ in more than 0.5eV. Does anyone have an answer for this? Any help will be very much appreciated. Cheers, Lara From owner-chemistry@ccl.net Mon Dec 12 09:23:01 2011 From: "=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= kacper.druzbicki^uj.edu.pl" To: CCL Subject: CCL:G: Error in frequencies calculation Message-Id: <-46023-111212091603-7781-NAioSUsPw91ipIX3eMDRdw]~[server.ccl.net> X-Original-From: =?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= Content-disposition: inline Content-language: pl Content-transfer-encoding: 7BIT Content-type: text/plain; CHARSET=US-ASCII Date: Mon, 12 Dec 2011 15:15:48 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= [kacper.druzbicki^uj.edu.pl] Dear CCL users, I am struggling with a quite demanding frequencies calculation for ~600 atomic system using ONIOM. I am going out of mind, since all the attempts had the same scenario. The job fails in the end with the following error: ... 3 vectors produced by pass 4 Test12= 8.87D-13 1.00D-09 XBig12= 4.13D-11 3.09D-07. 1 vectors produced by pass 5 Test12= 8.87D-13 1.00D-09 XBig12= 1.74D-16 1.09D-09. Applied DIIS recursively to reduced A of dimension 7038. DIIS for IP= 1 IOff= 50 NDo= 50 converged in 113 iterations. DIIS for IP= 5 IOff= 450 NDo= 50 converged in 112 iterations. DIIS for IP= 3 IOff= 350 NDo= 50 converged in 112 iterations. DIIS for IP= 4 IOff= 250 NDo= 50 converged in 112 iterations. DIIS for IP= 6 IOff= 400 NDo= 50 converged in 112 iterations. DIIS for IP= 8 IOff= 100 NDo= 50 converged in 112 iterations. DIIS for IP= 9 IOff= 200 NDo= 50 converged in 112 iterations. DIIS for IP= 2 IOff= 300 NDo= 50 converged in 113 iterations. DIIS for IP= 7 IOff= 150 NDo= 50 converged in 114 iterations. DIIS for IP= 0 IOff= 0 NDo= 50 converged in 126 iterations. DIIS for IP= 9 IOff= 800 NDo= 50 converged in 107 iterations. DIIS for IP= 1 IOff= 500 NDo= 50 converged in 109 iterations. DIIS for IP= 5 IOff= 550 NDo= 50 converged in 107 iterations. DIIS for IP= 3 IOff= 600 NDo= 50 converged in 113 iterations. DIIS for IP= 2 IOff= 850 NDo= 50 converged in 111 iterations. DIIS for IP= 8 IOff= 750 NDo= 50 converged in 113 iterations. DIIS for IP= 4 IOff= 650 NDo= 50 converged in 113 iterations. DIIS for IP= 7 IOff= 900 NDo= 50 converged in 113 iterations. DIIS for IP= 6 IOff= 700 NDo= 50 converged in 114 iterations. DIIS for IP= 0 IOff= 950 NDo= 50 converged in 114 iterations. DIIS for IP= 5 IOff= 1100 NDo= 50 converged in 108 iterations. DIIS for IP= 6 IOff= 1400 NDo= 50 converged in 108 iterations. DIIS for IP= 1 IOff= 1050 NDo= 50 converged in 108 iterations. DIIS for IP= 9 IOff= 1000 NDo= 50 converged in 113 iterations. DIIS for IP= 3 IOff= 1150 NDo= 50 converged in 113 iterations. DIIS for IP= 7 IOff= 1350 NDo= 50 converged in 107 iterations. DIIS for IP= 0 IOff= 1450 NDo= 50 converged in 113 iterations. DIIS for IP= 8 IOff= 1250 NDo= 50 converged in 112 iterations. DIIS for IP= 2 IOff= 1200 NDo= 50 converged in 113 iterations. DIIS for IP= 4 IOff= 1300 NDo= 50 converged in 113 iterations. DIIS for IP= 4 IOff= 1950 NDo= 6 converged in 106 iterations. DIIS for IP= 3 IOff= 1700 NDo= 50 converged in 113 iterations. DIIS for IP= 0 IOff= 1800 NDo= 50 converged in 112 iterations. DIIS for IP= 8 IOff= 1850 NDo= 50 converged in 114 iterations. DIIS for IP= 5 IOff= 1500 NDo= 50 converged in 112 iterations. DIIS for IP= 6 IOff= 1550 NDo= 50 converged in 113 iterations. DIIS for IP= 9 IOff= 1650 NDo= 50 converged in 112 iterations. DIIS for IP= 1 IOff= 1600 NDo= 50 converged in 111 iterations. DIIS for IP= 2 IOff= 1900 NDo= 50 converged in 109 iterations. DIIS for IP= 7 IOff= 1750 NDo= 50 converged in 113 iterations. FullF1: Do perturbations 1 to 3. NIJ > Max2 in MMCore. Error termination via Lnk1e ... I tried to get the frequencies both analytically and numerically but it resulted in the same error in both cases. I always gets 'NIJ > Max2 in MMCore.' error after 'FullF1: Do perturbations 1 to 3.' I found the info that the problem with 'NIJ > Max2 in MMCore.' has been solved in Gaussian09 Revision C.01. Unfortunately I still do not have this version. Do you know any alternative solution for this error? I lost a lot of time using Gaussian09 Revision B.01. With the best wishes, Casper Kacper Druzbicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Cracow, Poland phone: +48 12 6632265 From owner-chemistry@ccl.net Mon Dec 12 13:32:00 2011 From: "Mark Zottola mzottola(0)gmail.com" To: CCL Subject: CCL:G: PCM Question Message-Id: <-46024-111212132316-23503-HaqvDQpPpv3sy7ku4IBF3Q---server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=e89a8ff1c91e28b9b504b3e93a94 Date: Mon, 12 Dec 2011 13:23:11 -0500 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola#%#gmail.com] --e89a8ff1c91e28b9b504b3e93a94 Content-Type: text/plain; charset=ISO-8859-1 In optimizing a complex between two neutral molecules using PCM with the MPW1PW91 functional I receive the following message within Gaussian: PCMQM: There is more than one cavity, setting IComp=0. THis message is repeated several times during the SCF routine. I reach an energetic minimum and that minimum is different than if I optimize the structure excluding the PCM keyword. So my question is, what does this warning mean? Also, can I trust the energy minimum obtained with this warning? Thanks! Mark --e89a8ff1c91e28b9b504b3e93a94 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
In optimizing a complex between two neutral molecules using PCM with t= he MPW1PW91 functional I receive the following message within Gaussian:
=A0
=A0PCMQM: There is more than one cavity, setting IComp=3D0.
=A0
THis message is repeated several times during the SCF routine.=A0 I re= ach an energetic minimum and that minimum is different than if I optimize t= he structure excluding the PCM keyword.
So my question is, what does this warning mean?=A0 Also, can I trust t= he energy minimum obtained with this warning?
=A0
Thanks!
=A0
Mark
--e89a8ff1c91e28b9b504b3e93a94-- From owner-chemistry@ccl.net Mon Dec 12 15:44:00 2011 From: "Soren Eustis soreneustis^_^gmail.com" To: CCL Subject: CCL:G: PCM Question Message-Id: <-46025-111212154155-31416-HeHgdGz0wQpta+b9wjWuIQ|server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3406570905_25463798" Date: Mon, 12 Dec 2011 21:41:35 +0100 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_3406570905_25463798 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Mark, This is telling you that there is more than one cavity in the "solvent" model. Essentially, the PCM model is sensing that there are two distinct entities rather than a continuous system. Given that you are optimizing a vdW type complex, this message makes sense. The minimum you obtain with PCM should be different from the non-PCM (i.e. gas phase) optimization as the local environment is, by definition, different in that case. Kudos on your choice of functional. I have been a believer in the mPW1PW91 for years and it is certainly appropriate for vdW systems. Best, Soren Soren N. Eustis, Ph.D. ETH =AD Z=FCrich Institute for Biogeochemistry and Pollutant Dynamics CHN F33 Universit=E4tstrasse 16 8092 Z=FCrich Switzerland +41 44 632 9348 (Office) +41 44 632 1438(Fax) soren*o*env.ethz.ch =20 > From: "Mark Zottola mzottola(0)gmail.com" Reply-To: Ccl Date: Mon, 12 Dec 2011 13:23:11 -0500 To: Soren Eustis Subject: CCL:G: PCM Question In optimizing a complex between two neutral molecules using PCM with the MPW1PW91 functional I receive the following message within Gaussian: =20 PCMQM: There is more than one cavity, setting IComp=3D0. =20 THis message is repeated several times during the SCF routine. I reach an energetic minimum and that minimum is different than if I optimize the structure excluding the PCM keyword. So my question is, what does this warning mean? Also, can I trust the energy minimum obtained with this warning? =20 Thanks! =20 Mark --B_3406570905_25463798 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable
Mark,
   This is telling you that there is more than one cav= ity in the "solvent" model.  Essentially, the PCM model is sensing that= there are two distinct entities rather than a continuous system.  Give= n that you are optimizing a vdW type complex, this message makes sense. &nbs= p;

   The minimum you obtain with PCM sho= uld be different from the non-PCM (i.e. gas phase) optimization as the local= environment is, by definition, different in that case.  
   Kudos on your choice of functional.  I have be= en a believer in the mPW1PW91 for years and it is certainly appropriate for = vdW systems.

Best,

Soren


Soren N. Eustis, Ph.D.=
ETH – Z=FCrich
Institute for Biogeochemistry and Po= llutant Dynamics
CHN F33
Universit=E4tstrasse 16
From: "Mark Zottola mzottola(0)gmail.com" <owner-chemistry*o*ccl.net>
Reply-To: Ccl <ch= emistry*o*ccl.net>
Date: Mon,= 12 Dec 2011 13:23:11 -0500
To: So= ren Eustis <soreneustis*o*gmail.com<= /a>>
Subject: CCL:G: PCM Questi= on

--B_3406570905_25463798-- From owner-chemistry@ccl.net Mon Dec 12 16:18:00 2011 From: "Soren Eustis soreneustis_+_gmail.com" To: CCL Subject: CCL: TD-DFT vertical spectrum vs geometry optimization Message-Id: <-46026-111212161624-30377-Y2rcXl1SFYz+0EnSu9e9jw()server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 12 Dec 2011 22:16:10 +0100 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis=gmail.com] There are several issues here. The first step is a (U)DFT optimization to a local (T1) minimum. This will give you an absolute triplet (T1) energy and structure. The second step is using a triplet geometry as a singlet minimum, which is incorrect. To perform a TD-DFT optimization, you need to start with a minimum structure. In your case, you are using the triplet geometry and assigning it a singlet multiplicity (i.e. 0 1). If you wanted to find the T2 vertical energy, you could do this by changing your charge/multiplicity keyword to 0 3, leaving the rest unchanged. To get a vertical triplet energy, you could perform an S0 optimization followed by a single point energy using that structure with the 0 3 charge/multiplicity card. However, vertical triplet energies are normally performed in reverse. Optimize the T1 geometry (UDFT or RODFT), then perform a single point calculation with the 0 1 card. This would yield values of interest for phosphorescence studies. On 12/12/11 11:10 , "LARA MARTINEZ FERNANDEZ lara.martinez!A!uam.es" wrote: > >Sent to CCL by: "LARA MARTINEZ FERNANDEZ" [lara.martinez_+_uam.es] >Dear CCLers, > >We are trying to optimize the first excited triplet of a Au complex. For >this, we have performed a >UPBE1PBE geometry optimization. > >#P PBE1PBE/gen pseudo=read opt POP=FULL GFINPUT GFPRINT IOP(6/7=3) > >Title Card Required > >0 3 >.. > > >On the optimized geometry we have performed a TD-PBE1PBE calculation. > >#P PBE1PBE/gen pseudo=read TD(triplets,NStates=5) POP=FULL GFINPUT >GFPRINT IOP(6/7=3) >scf=tight > >Title Card Required > >0 1 >.. > >We were expecting to obtain the same energy from the geometry >optimization and from the first >TD-DFT root, but these energies in fact differ in more than 0.5eV. > >Does anyone have an answer for this? > >Any help will be very much appreciated. > >Cheers, > >Lara> >