From owner-chemistry@ccl.net Thu Aug 18 04:59:00 2011 From: "Thomas Gkourmpis thomas.gkourmpis-x-borealisgroup.com" To: CCL Subject: CCL: NAMD Recommendation question Message-Id: <-45275-110818045748-26817-e/YWEQeB5iJ00RmQUhXN2A_-_server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Thu, 18 Aug 2011 04:57:44 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis#%#borealisgroup.com] Hello everyone I am trying to get a molecular dynamics package together with a molecular builder/viewer for molecule preparation and data analysis. My main area of work will be in polymers and I am interested in both equilibrium and non-equilibrium properties. I came across NAMD/VMD and I was wondering if anyone has used it and can provide some comments on the level of user-friendliness, accuracy of calculations, speed, flexibility etc. Practically would you recommend the program or I should look for something else? Thanks a lot in advance Thomas Gkourmpis 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 From owner-chemistry@ccl.net Thu Aug 18 06:46:00 2011 From: "Vera Cathrine vera.cathrine,,yahoo.com" To: CCL Subject: CCL: G09: CASSCF Message-Id: <-45276-110817105544-2422-v4FPVbDUbwMWPbUneHWJ4w|server.ccl.net> X-Original-From: "Vera Cathrine" Date: Wed, 17 Aug 2011 10:55:42 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine(_)yahoo.com] Dear CCL Users, I am trying to study the photochemical reaction of an organic system using CASSCF. The full pi active space in this organic compound is very large (>14 pi electrons). I like to reduce this to smaller CAS (< CAS(8,8)) for doing excited state dynamics. I am not pretty sure how to choose the orbitals for the small active space. I am trying to reduce the active space step by step for both S0 and S1.I read the guess from rhf calculation and a small basis set (according to Mike robb web page). I swap the orbitals based on visual inspection (chemical intuition) and following occupation numbers. I exclude the orbitals with closest value to 0 or 2 in every step. Is this a good way to reduce the active space? Which orbitals are more proper for this purpose (Natural or canonical orbitals)? Why? Any suggestion or pointer to literature is welcome. Kind wishes, Vera Cathrine From owner-chemistry@ccl.net Thu Aug 18 08:38:00 2011 From: "Jason Swails swails[a]qtp.ufl.edu" To: CCL Subject: CCL: NAMD Recommendation question Message-Id: <-45277-110818083026-2316-qHW0w21DN6Ce71lc+xnEkw#server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=00504502c1c56e451504aac6c61d Date: Thu, 18 Aug 2011 08:30:16 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails++qtp.ufl.edu] --00504502c1c56e451504aac6c61d Content-Type: text/plain; charset=ISO-8859-1 On Thu, Aug 18, 2011 at 4:57 AM, Thomas Gkourmpis thomas.gkourmpis-x-borealisgroup.com wrote: > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis#%#borealisgroup.com] > Hello everyone > > I am trying to get a molecular dynamics package together with a molecular > builder/viewer for molecule preparation and data analysis. My main area of > work will be in polymers and I am interested in both equilibrium and > non-equilibrium properties. > > I came across NAMD/VMD and I was wondering if anyone has used it and can > provide some comments on the level of user-friendliness, accuracy of > calculations, speed, flexibility etc. Practically would you recommend the > program or I should look for something else? > VMD is a wonderful program, in my opinion (and experience). There's a little bit of a learning curve, but it's flexible, powerful, and well supported through online help mailing list(s) if you need it. I've never used NAMD (I'm an Amber user myself) but I know several people that do, and they're big fans of it. I'm obviously biased toward Amber after having used it so much the past couple years, but NAMD should be reasonably straightforward to use, and VMD does link into it nicely as I've been told, giving you access to a sophisticated GUI when running your MD simulations (not particularly common throughout the MD world). Hope this helps, Jason -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --00504502c1c56e451504aac6c61d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Thu, A= ug 18, 2011 at 4:57 AM, Thomas Gkourmpis thomas.gkourmpis-x-borealisgroup.com <owner-chemistry++ccl.ne= t> wrote:

Sent to CCL by: "Thomas =A0Gkourmpis" [thomas.gkourmpis#%#borealisgroup.com]
Hello everyone

I am trying to get a molecular dynamics package together with a molecular b= uilder/viewer for molecule preparation and data analysis. My main area of w= ork will be in polymers and I am interested in both equilibrium and non-equ= ilibrium properties.

I came across NAMD/VMD and I was wondering if anyone has used it and can pr= ovide some comments on the level of user-friendliness, accuracy of calculat= ions, speed, flexibility etc. Practically would you recommend the program o= r I should look for something else?

VMD is a wonderful program, in my opinion (and experi= ence).=A0 There's a little bit of a learning curve, but it's flexib= le, powerful, and well supported through online help mailing list(s) if you= need it.=A0 I've never used NAMD (I'm an Amber user myself) but I = know several people that do, and they're big fans of it.=A0 I'm obv= iously biased toward Amber after having used it so much the past couple yea= rs, but NAMD should be reasonably straightforward to use, and VMD does link= into it nicely as I've been told, giving you access to a sophisticated= GUI when running your MD simulations (not particularly common throughout t= he MD world).

Hope this helps,
Jason

--
Jason M. Swails
= Quantum Theory Project,
University of Florida
Ph.D. Graduate Student<= br>352-392-4032
--00504502c1c56e451504aac6c61d-- From owner-chemistry@ccl.net Thu Aug 18 09:24:01 2011 From: "turker akcay turkerakcay]*[hotmail.com" To: CCL Subject: CCL:G: TED calculation Message-Id: <-45278-110818092200-9000-4zD1IvDnHVA7hXWtGT4Xhw++server.ccl.net> X-Original-From: "turker akcay" Date: Thu, 18 Aug 2011 09:21:56 -0400 Sent to CCL by: "turker akcay" [turkerakcay|-|hotmail.com] I am a gaussian user. How can I calculate TED of vibrational modes (total energy distrubution). I read a software (SQM V.1.0.) in literature but I couldn't find it on web. Could you help me about free software or calculation methods of the TED. Thanks in advance... From owner-chemistry@ccl.net Thu Aug 18 13:06:01 2011 From: "Van Dam, Hubertus J HubertusJJ.vanDam],[pnnl.gov" To: CCL Subject: CCL: G09: CASSCF Message-Id: <-45279-110818120711-29212-4HyiBXQ1PrwhYvvtq2TXoQ]=[server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 Aug 2011 09:07:02 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam~!~pnnl.gov] Hi Vera, This is a rather tricky situation. If you want to pick active orbitals automatically than using natural orbitals and selecting them based on occupation numbers is to be preferred over canonical orbitals. The reason being that orbitals with high occupation numbers give the best approximation to the wavefunction in some perturbative sense (I don't happen to have a reference handy). The main issue I see with this approach is that you need to calculate a wavefunction with more active orbitals to start with so that you can sensibly select the ones which are not fully occupied but significantly occupied. I.e. if you somehow force an orbital to be empty then it does not make much sense to discard that orbital based on its low occupation number. The second issue is that you are running dynamics. For sensible dynamics runs you need the conservation of energy to hold. If at some point of the potential energy surface the selection algorithm changes the manyfold of the active orbitals due to its discreet choices, you typically lose accuracy in the conservation of energy. This may cause problems in your simulation. I hope this helps, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov|ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov|ccl.net] On Behalf Of Vera Cathrine vera.cathrine,,yahoo.com Sent: Wednesday, August 17, 2011 7:56 AM To: Van Dam, Hubertus J Subject: CCL: G09: CASSCF Sent to CCL by: "Vera Cathrine" [vera.cathrine(_)yahoo.com] Dear CCL Users, I am trying to study the photochemical reaction of an organic system using CASSCF. The full pi active space in this organic compound is very large (>14 pi electrons). I like to reduce this to smaller CAS (< CAS(8,8)) for doing excited state dynamics. I am not pretty sure how to choose the orbitals for the small active space. I am trying to reduce the active space step by step for both S0 and S1.I read the guess from rhf calculation and a small basis set (according to Mike robb web page). I swap the orbitals based on visual inspection (chemical intuition) and following occupation numbers. I exclude the orbitals with closest value to 0 or 2 in every step. Is this a good way to reduce the active space? Which orbitals are more proper for this purpose (Natural or canonical orbitals)? Why? Any suggestion or pointer to literature is welcome. Kind wishes, Vera Cathrinehttp://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 Thu Aug 18 13:40:01 2011 From: "Adel El-Azhary azhary---ksu.edu.sa" To: CCL Subject: CCL: What is wrong with M06 vibrational frequencies Message-Id: <-45280-110818093030-29480-kG5VhhWi3X2YezC8xLlChw a server.ccl.net> X-Original-From: "Adel El-Azhary" Date: Thu, 18 Aug 2011 09:30:27 -0400 Sent to CCL by: "Adel El-Azhary" [azhary(!)ksu.edu.sa] Hi All I am not sure that anyone of you experienced this problem before or knows a solution for it. I am calculating vibrational frequencies at the HF, B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All vibrational frequencies are real at the HF, B3LYP and MP2 levels but at the M06, M06L, M062x and M06HF levels, one or more vibrational frequency is imaginary. I have been told that the integration grids might be the cause of this problem. I tried different integration grids without much success. Does anyone know what to do or why is this. The idea that the molecule is not at the global minimum structure I doubt that it is correct at all. At least I do geometry optimization first. Adel El-Azhary King Saud University Saudi Arabia From owner-chemistry@ccl.net Thu Aug 18 14:15:00 2011 From: "Adam Tenderholt atenderholt!^!gmail.com" To: CCL Subject: CCL: NWChem: print options Message-Id: <-45281-110818134727-28839-kt2YMBDyE0MtFOL8fZ67Ng[#]server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Aug 2011 10:47:18 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt ~~ gmail.com] Hi CCLers, I'm starting to learn NWChem, but can't figure out how to get more information printed in the output file, even after looking at the wiki. Is it possible to print the one-electron overlap matrix and the eigenvalues for all of the orbitals? If I use "print high", I can get eigenvalues for only the occupied plus 10 virtual orbitals. What about orbital symmetries? I've tried 'print "final vector symmetries"' in the DFT section with no luck. And is it possible to print which basis functions map to which atoms and orbital type? Thanks, Adam From owner-chemistry@ccl.net Thu Aug 18 14:50:01 2011 From: "Rajarshi Guha rajarshi.guha!^!gmail.com" To: CCL Subject: CCL: CINFLash (ACS National Meeting, Denver, Fall 2011) Message-Id: <-45282-110818134924-30351-oFUubBI8b8HYIDholY4Ciw+/-server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Aug 2011 13:49:17 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha ~ gmail.com] With the ACS coming up, we are running CINFlash once again - a session of 8 minute lightning talks on any aspect of chemical information and cheminformatics. It's going to be at 1:30pm, Wednesday, August 31st, 2011 in Room 112 of the Colorado Convention Center. As before, we aren't using PACS. We've extended our deadline so we're going to be accepting abstracts till the August 26, 2011. If you'd like to participate, send a short (< 100 words) to cinf.flash(-)gmail.com. Visit http://acscinf.org/meetings/242/calls/flash242.php for more details. If you have any questions mail me at rajarshi.guha(-)gmail.com -- Rajarshi Guha Chair Elect CINF From owner-chemistry@ccl.net Thu Aug 18 15:26:01 2011 From: "Carlos Andres Jimenez qcarlos04:_:gmail.com" To: CCL Subject: CCL:G: Stuttgart pseudopotentials Message-Id: <-45283-110818120744-29316-dptICmaajcF4SbQRZJHVMA,server.ccl.net> X-Original-From: "Carlos Andres Jimenez" Date: Thu, 18 Aug 2011 12:07:42 -0400 Sent to CCL by: "Carlos Andres Jimenez" [qcarlos04,gmail.com] Hi I'm interested in working with Stuttgart's pseudopotentials in a system composed by carbon, hydrogen and iron. I want to work with the pseudopotential on the metal. Could anyone help me about input file details in gaussian 09, please? Thank you very much for your help. Kind Regards Carlos Jimenez Chemistry student Universidad de Antioquia colombia From owner-chemistry@ccl.net Thu Aug 18 16:01:01 2011 From: "Soren Eustis soreneustis^-^gmail.com" To: CCL Subject: CCL: What is wrong with M06 vibrational frequencies Message-Id: <-45284-110818145201-420-UGblJhHCRhLlm/aY0tUb9g---server.ccl.net> X-Original-From: Soren Eustis Content-Transfer-Encoding: 8bit Content-type: text/plain; charset="ISO-8859-1" Date: Thu, 18 Aug 2011 20:51:45 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis ~ gmail.com] Adel, Am I correct in my understanding that you are optimizing the geometry with each functional, then calculating the frequency with the same functional and basis set used to determine the ground state structure? The frequency calculation should be performed with the exact model chemistry as used for the geometry optimization (including the grid density). You may be doing this already, but it is unclear from your post. Best, Soren Soren N. Eustis, Ph.D. ETH ­ Zürich Environmental Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universitätstrasse 16 CHN F33 8092 ZürichSWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren~~env.ethz.ch On 8/18/11 15:30 , "Adel El-Azhary azhary---ksu.edu.sa" wrote: > >Sent to CCL by: "Adel El-Azhary" [azhary(!)ksu.edu.sa] > >Hi All >I am not sure that anyone of you experienced this problem before or knows >a solution for it. I am calculating vibrational frequencies at the HF, >B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All >vibrational frequencies are real at the HF, B3LYP and MP2 levels but at >the M06, M06L, M062x and M06HF levels, one or more vibrational frequency >is imaginary. I have been told that the integration grids might be the >cause of this problem. I tried different integration grids without much >success. Does anyone know what to do or why is this. The idea that the >molecule is not at the global minimum structure I doubt that it is >correct at all. At least I do geometry optimization first. > >Adel El-Azhary >King Saud University >Saudi Arabia> > From owner-chemistry@ccl.net Thu Aug 18 16:35:00 2011 From: "Van Dam, Hubertus J HubertusJJ.vanDam##pnnl.gov" To: CCL Subject: CCL: What is wrong with M06 vibrational frequencies Message-Id: <-45285-110818161235-15135-kUVK9JsSt7gUrbvj1Qs8pg_-_server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 Aug 2011 13:12:25 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam.:.pnnl.gov] Hi Adel, I am not entirely sure but it seems that all the functionals that you are having problems with are Meta-GGAs. I.e. they depend on the electron density, density gradient and the kinetic energy density. Information that has been provided to me in the past is that you need more extensive quadrature grids to represent the kinetic energy terms accurately. So that might have something to do with this. Another potential issue is that you need special terms that relate to the kinetic energy contributions. For the 1st derivatives that is not so bad, but the higher the order of the derivatives you are trying to evaluate the more rapidly the number of terms grow with the number of quantities that go into the functional. Hence also the likelihood of a coding error increases. How to distinguish these possibilities? Maybe the first thing to try is to calculate frequencies numerically. If those seem much more robust than your analytic frequencies then maybe there is coding error, if not then maybe it is simply the quadrature accuracy. Good luck, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov-.-ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov-.-ccl.net] On Behalf Of Adel El-Azhary azhary---ksu.edu.sa Sent: Thursday, August 18, 2011 6:30 AM To: Van Dam, Hubertus J Subject: CCL: What is wrong with M06 vibrational frequencies Sent to CCL by: "Adel El-Azhary" [azhary(!)ksu.edu.sa] Hi All I am not sure that anyone of you experienced this problem before or knows a solution for it. I am calculating vibrational frequencies at the HF, B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All vibrational frequencies are real at the HF, B3LYP and MP2 levels but at the M06, M06L, M062x and M06HF levels, one or more vibrational frequency is imaginary. I have been told that the integration grids might be the cause of this problem. I tried different integration grids without much success. Does anyone know what to do or why is this. The idea that the molecule is not at the global minimum structure I doubt that it is correct at all. At least I do geometry optimization first. Adel El-Azhary King Saud University Saudi Arabiahttp://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 Thu Aug 18 17:10:01 2011 From: "Adel El-Azhary azhary]![KSU.EDU.SA" To: CCL Subject: CCL: What is wrong with M06 vibrational frequencies Message-Id: <-45286-110818163351-7461-Ovk+MVqsl0l6ZmSugkDIhw|server.ccl.net> X-Original-From: Adel El-Azhary Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 18 Aug 2011 23:31:01 +0300 MIME-Version: 1.0 Sent to CCL by: Adel El-Azhary [azhary-x-KSU.EDU.SA] Soren, Yes, I am doing geometry optimization and frequency calculation with the same basis set and integration grids. ________________________________________ > From: owner-chemistry+azhary==ksu.edu.sa|a|ccl.net [owner-chemistry+azhary==ksu.edu.sa|a|ccl.net] On Behalf Of Soren Eustis soreneustis^-^gmail.com [owner-chemistry|a|ccl.net] Sent: Thursday, August 18, 2011 9:51 PM To: Adel El-Azhary Subject: CCL: What is wrong with M06 vibrational frequencies Sent to CCL by: Soren Eustis [soreneustis ~ gmail.com] Adel, Am I correct in my understanding that you are optimizing the geometry with each functional, then calculating the frequency with the same functional and basis set used to determine the ground state structure? The frequency calculation should be performed with the exact model chemistry as used for the geometry optimization (including the grid density). You may be doing this already, but it is unclear from your post. Best, Soren Soren N. Eustis, Ph.D. ETH ­ Zürich Environmental Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universitätstrasse 16 CHN F33 8092 ZürichSWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren(_)env.ethz.ch On 8/18/11 15:30 , "Adel El-Azhary azhary---ksu.edu.sa" wrote: > >Sent to CCL by: "Adel El-Azhary" [azhary(!)ksu.edu.sa] > >Hi All >I am not sure that anyone of you experienced this problem before or knows >a solution for it. I am calculating vibrational frequencies at the HF, >B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All >vibrational frequencies are real at the HF, B3LYP and MP2 levels but at >the M06, M06L, M062x and M06HF levels, one or more vibrational frequency >is imaginary. I have been told that the integration grids might be the >cause of this problem. I tried different integration grids without much >success. Does anyone know what to do or why is this. The idea that the >molecule is not at the global minimum structure I doubt that it is >correct at all. At least I do geometry optimization first. > >Adel El-Azhary >King Saud University >Saudi Arabiahttp://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 Thu Aug 18 18:24:01 2011 From: "Adam Tenderholt atenderholt{:}gmail.com" To: CCL Subject: CCL:G: Stuttgart pseudopotentials Message-Id: <-45287-110818182243-26376-u42KCBHYc17zrgz7Sakpnw^^^server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Aug 2011 15:22:34 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt%a%gmail.com] Hi Carlos (and others), I believe you need to have something like #B3LYP/SDD pseudo=read with the following after your input coordinates BLANK_LINE Fe 0 SDD BLANK_LINE (Replace BLANK_LINE with an empty line...). Hope that helps, Adam On Thu, Aug 18, 2011 at 9:07 AM, Carlos Andres Jimenez qcarlos04:_:gmail.com wrote: > > Sent to CCL by: "Carlos Andres Jimenez" [qcarlos04,gmail.com] > Hi > > I'm interested in working with Stuttgart's pseudopotentials in a system composed by carbon, hydrogen and iron. I want to work with the pseudopotential on the metal. > > Could anyone help me about input file details in gaussian 09, please? > > Thank you very much for your help. > > Kind Regards > > > Carlos Jimenez > Chemistry student > Universidad de Antioquia > colombia>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Aug 18 18:59:00 2011 From: "Adam Tenderholt atenderholt[#]gmail.com" To: CCL Subject: CCL:G: What is wrong with M06 vibrational frequencies Message-Id: <-45288-110818183140-7274-MymRVMRwFi8gHCaco9PvAQ=server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Aug 2011 15:31:31 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt!=!gmail.com] Hi Adel, (I'm assuming you're using Gaussian. If not, adjust as necessary for other packages.) Are you using Opt=Tight and Int=UltraFine? That usually does it for me. You could also try Opt=(Tight,ReadFC) and provide a checkpoint file from the frequency calculation with imaginary modes. Adam On Thu, Aug 18, 2011 at 1:31 PM, Adel El-Azhary azhary]![KSU.EDU.SA wrote: > > Sent to CCL by: Adel El-Azhary [azhary-x-KSU.EDU.SA] > Soren, > > Yes, I am doing geometry optimization and frequency calculation with the same basis set and integration grids. > > ________________________________________ >> From: owner-chemistry+azhary==ksu.edu.sa#,#ccl.net [owner-chemistry+azhary==ksu.edu.sa#,#ccl.net] On Behalf Of Soren Eustis soreneustis^-^gmail.com [owner-chemistry#,#ccl.net] > Sent: Thursday, August 18, 2011 9:51 PM > To: Adel El-Azhary > Subject: CCL: What is wrong with M06 vibrational frequencies > > Sent to CCL by: Soren Eustis [soreneustis ~ gmail.com] > Adel, > >    Am I correct in my understanding that you are optimizing the geometry > with each functional, then calculating the frequency with the same > functional and basis set used to determine the ground state structure? > >    The frequency calculation should be performed with the exact model > chemistry as used for the geometry optimization (including the grid > density).  You may be doing this already, but it is unclear from your post. > > Best, > > Soren > > Soren N. Eustis, Ph.D. > ETH ­ Zürich > Environmental Chemistry Group > Institute for Biogeochemistry and Pollutant Dynamics > Universitätstrasse 16 > CHN F33 > 8092 ZürichSWITZERLAND > > +41 44 632 93 48 (office) > +41 44 632 14 38 (fax) > > soren(_)env.ethz.ch > > > > > On 8/18/11 15:30 , "Adel El-Azhary azhary---ksu.edu.sa" > wrote: > >> >>Sent to CCL by: "Adel  El-Azhary" [azhary(!)ksu.edu.sa] >> >>Hi All >>I am not sure that anyone of you experienced this problem before or knows >>a solution for it. I am calculating vibrational frequencies at the HF, >>B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All >>vibrational frequencies are real at the HF, B3LYP and MP2 levels but at >>the M06, M06L, M062x and M06HF levels, one or more vibrational frequency >>is imaginary. I have been told that the integration grids might be the >>cause of this problem. I tried different integration grids without much >>success. Does anyone know what to do or why is this. The idea that the >>molecule is not at the global minimum structure I doubt that it is >>correct at all. At least I do geometry optimization first. >> >>Adel El-Azhary >>King Saud University >>Saudi Arabiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Aug 18 22:28:01 2011 From: "Adel El-Azhary azhary=KSU.EDU.SA" To: CCL Subject: CCL:G: What is wrong with M06 vibrational frequencies Message-Id: <-45289-110818222502-8591-gXpq46e1wsQrCYs7SxiM9Q]![server.ccl.net> X-Original-From: Adel El-Azhary Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 19 Aug 2011 05:22:40 +0300 MIME-Version: 1.0 Sent to CCL by: Adel El-Azhary [azhary%a%KSU.EDU.SA] Adam, Really thanks for your advise, but this did not work either. "Int=UltraFine" is what is supposed to work in such cases but it did not work for me. ________________________________________ > From: owner-chemistry+azhary==ksu.edu.sa/a\ccl.net [owner-chemistry+azhary==ksu.edu.sa/a\ccl.net] On Behalf Of Adam Tenderholt atenderholt[#]gmail.com [owner-chemistry/a\ccl.net] Sent: Friday, August 19, 2011 1:31 AM To: Adel El-Azhary Subject: CCL:G: What is wrong with M06 vibrational frequencies Sent to CCL by: Adam Tenderholt [atenderholt!=!gmail.com] Hi Adel, (I'm assuming you're using Gaussian. If not, adjust as necessary for other packages.) Are you using Opt=Tight and Int=UltraFine? That usually does it for me. You could also try Opt=(Tight,ReadFC) and provide a checkpoint file from the frequency calculation with imaginary modes. Adam On Thu, Aug 18, 2011 at 1:31 PM, Adel El-Azhary azhary]![KSU.EDU.SA wrote: > > Sent to CCL by: Adel El-Azhary [azhary-x-KSU.EDU.SA] > Soren, > > Yes, I am doing geometry optimization and frequency calculation with the same basis set and integration grids. > > ________________________________________ >> From: owner-chemistry+azhary==ksu.edu.sa#,#ccl.net [owner-chemistry+azhary==ksu.edu.sa#,#ccl.net] On Behalf Of Soren Eustis soreneustis^-^gmail.com [owner-chemistry#,#ccl.net] > Sent: Thursday, August 18, 2011 9:51 PM > To: Adel El-Azhary > Subject: CCL: What is wrong with M06 vibrational frequencies > > Sent to CCL by: Soren Eustis [soreneustis ~ gmail.com] > Adel, > > Am I correct in my understanding that you are optimizing the geometry > with each functional, then calculating the frequency with the same > functional and basis set used to determine the ground state structure? > > The frequency calculation should be performed with the exact model > chemistry as used for the geometry optimization (including the grid > density). You may be doing this already, but it is unclear from your post. > > Best, > > Soren > > Soren N. Eustis, Ph.D. > ETH ­ Zürich > Environmental Chemistry Group > Institute for Biogeochemistry and Pollutant Dynamics > Universitätstrasse 16 > CHN F33 > 8092 ZürichSWITZERLAND > > +41 44 632 93 48 (office) > +41 44 632 14 38 (fax) > > soren(_)env.ethz.ch > > > > > On 8/18/11 15:30 , "Adel El-Azhary azhary---ksu.edu.sa" > wrote: > >> >>Sent to CCL by: "Adel El-Azhary" [azhary(!)ksu.edu.sa] >> >>Hi All >>I am not sure that anyone of you experienced this problem before or knows >>a solution for it. I am calculating vibrational frequencies at the HF, >>B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All >>vibrational frequencies are real at the HF, B3LYP and MP2 levels but at >>the M06, M06L, M062x and M06HF levels, one or more vibrational frequency >>is imaginary. I have been told that the integration grids might be the >>cause of this problem. I tried different integration grids without much >>success. Does anyone know what to do or why is this. The idea that the >>molecule is not at the global minimum structure I doubt that it is >>correct at all. At least I do geometry optimization first. >> >>Adel El-Azhary >>King Saud University >>Saudi Arabiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt