From owner-chemistry@ccl.net Tue Oct 14 04:52:01 2008 From: "Mahmoud Korani Abdel-Latif mkkhedr**hotmail.com" To: CCL Subject: CCL: Molecular Dynamics Message-Id: <-37906-081014044823-4088-g+bOJAsHUFZje39bJoPcpg#,#server.ccl.net> X-Original-From: "Mahmoud Korani Abdel-Latif" Date: Tue, 14 Oct 2008 04:48:18 -0400 Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr a hotmail.com] Dear CCLers, First, thanks in advance Second, I would like to do molecular simulation for some bio crystals using CPMD program but unfortunately, it is the first time to me to make molecular dynamics. So I need some simple available references to learn about MD. Is it available to do molecular dynamics for crystals or not? What should I start with? Thanks again. Best Regards From owner-chemistry@ccl.net Tue Oct 14 10:39:01 2008 From: "Maria Rudbeck maru^physto.se" To: CCL Subject: CCL: charge+modredundant Message-Id: <-37907-081014103627-10075-n+Ozm/18DBLnSHt+qIhqcg[a]server.ccl.net> X-Original-From: "Maria Rudbeck" Date: Tue, 14 Oct 2008 10:36:23 -0400 Sent to CCL by: "Maria Rudbeck" [maru-*-physto.se] Hello CCL users! I have a question with several different parts: 1. Are the coordinates of point charges fixed? 2. If not, is it possible to fix the bond distance between a point charge and an atom? If yes, what is the input? I know that you can fix the coordinates of a point charge and the coordinates of an atom. However, this is of no interest to me, since I want to use 2 or more positive charges without constraining the molecule. 3. Is the repulsive term in the charge defaulted to zero, i.e. is A=0? And what is the definition of the fixed field? In fact, any comments on these items would be very appreciated. 4. Somebody mentioned that you could use ghost atoms as charges - is this true? If yes, how does it work? My question relates to how the environment affects a molecule in terms of bond distances and force constants. My option is to use cations, however this means a larger frequency calculation... I know this is a long question, any remarks would be appreciated! Kind Regards, Maria Rudbeck maru _ physto.se From owner-chemistry@ccl.net Tue Oct 14 13:31:01 2008 From: "Shina Lynn Kamerlin skamerli]*[usc.edu" To: CCL Subject: CCL:G: Gaussian Thermochemistry Message-Id: <-37908-081013190400-360-8jw26Kxcgumhn/98xH6KSQ[*]server.ccl.net> X-Original-From: "Shina Lynn Kamerlin" Date: Mon, 13 Oct 2008 19:03:56 -0400 Sent to CCL by: "Shina Lynn Kamerlin" [skamerli]=[usc.edu] Dear all, I have a quick query regarding gaussian thermochemistry output. I am trying to look at gas phase entropies, particularly the entropy decomposition (i.e. translational, rotational, vibrational) from standard gaussian thermochemistry calculations. I am looking at large-ish systems, and the numbers I got seemed very strange, so I decided to try something very simple, just dimerisation of F2 to see if what I am doing is working. For dimerisation, I think I would expect ~10kcal/mol, except, what I get is quite strange: Entropy F2 F Translational 10.8 10.4 Rotational 3.4 0.0 Vibrational 0.04 0.0 Total 14.2 10.4 (these are in kcal/mol, assuming 298K, taken from the cal/mol-kelvin value given in the gaussian output). I am clearly doing something wrong, I just have no idea what. Any advice/suggestions would be hugely appreciated! Thanks, Lynn From owner-chemistry@ccl.net Tue Oct 14 14:48:00 2008 From: "Agrafiotis, Dimitris K. PRDUS DAGRAFIO()its.jnj.com" To: CCL Subject: CCL: REMINDER: OASYS deadline for CINF Symposium on Adaptive Scoring Functions rapidly approaching (Oct. 20) Message-Id: <-37909-081014120415-25555-PQGpG1Rv7ihgw84RWXtJxA+/-server.ccl.net> X-Original-From: "Agrafiotis, Dimitris K. [PRDUS]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C92E11.F74AA93A" Date: Tue, 14 Oct 2008 11:31:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Agrafiotis, Dimitris K. [PRDUS]" [DAGRAFIO-$-its.jnj.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C92E11.F74AA93A Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Special CINF Symposium at Spring ACS National Meeting on Adaptive Scoring Functions, March 22-26, 2009, Salt Lake City, Utah Dear colleagues, This is a reminder that Oct. 20 is the deadline for submitting abstracts for the Adaptive Scoring Functions Symposium at the next ACS National Meeting in Salt Lake City. If you are interested in presenting your work and have not yet submitted an abstract, please do so at your earliest convenience though the OASYS web site: http://oasys.acs.org/. The symposium is listed under the CINF division. We are looking forward to your contributions and to seeing you all in Salt Lake City. Eric Martin & Dimitris Agrafiotis ------_=_NextPart_001_01C92E11.F74AA93A Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable REMINDER: OASYS deadline for CINF Symposium on Adaptive Scoring = Functions rapidly approaching (Oct. 20)

Special CINF = Symposium at Spring ACS National Meeting on Adaptive Scoring Functions, March 22-26, 2009, Salt Lake City, = Utah

Dear = colleagues,

This is a = reminder that Oct. 20 is = the deadline for submitting = abstracts for the Adaptive Scoring Functions = Symposium at the next ACS National Meeting in Salt Lake = City. If you = are interested in presenting your work and have not yet submitted an abstract, please do so at your earliest = convenience = though the OASYS web site: http://oasys.acs.org/. = The symposium is listed under the CINF division. We are looking forward to your = contributions and to seeing you all in Salt Lake City.

Eric Martin & Dimitris = Agrafiotis

------_=_NextPart_001_01C92E11.F74AA93A-- From owner-chemistry@ccl.net Tue Oct 14 16:27:00 2008 From: "errol lewars elewars!=!trentu.ca" To: CCL Subject: CCL: Small molecules with HF SCF convergence difficulty Message-Id: <-37910-081014135606-15822-HPX2Rwt9q5nYQeRkWcA16Q ~~ server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Oct 2008 12:56:43 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars() trentu.ca] 2008 Oct 14 Hello, Some of these refs may be relevant: 1) A black-box [convergence] algorithm K N Kudin, et al, J Chem Phys, 2002, 116, 8255 2) M Defranceschi, C Le Bris, J Mathematical Chem, 1997, 21, 1 3) M Defranceschi, C Le Bris, Int J Quantum Chem, 1999, 71, 227 4) G Berthier et al, Int J Quantum Chem, 2003, 93, 156 Also, transition metals are said to be good at aggravating HF convergence problems; and the CCL archives have some convergence problems postings. E Lewars ==== Adam Hunter spacyhunter{=}gmail.com wrote: > > Sent to CCL by: Adam Hunter [spacyhunter#gmail.com] > hi, all, > I'm studying the SCF convergence problem. Can anybody provide me > some small molecules which are hard to converge with the Hartree-Fock > method? I know several such examples with DFT convergence difficulty, > but have not found good examples for the Hartree-Fock method. > Any help will be greatly appreciated. Thank you very much! > all the best > Adamhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Tue Oct 14 17:02:00 2008 From: "Van Dam, HJJ \(Huub\) huub.van-dam::stfc.ac.uk" To: CCL Subject: CCL: Small molecules with HF SCF convergence difficulty Message-Id: <-37911-081014055000-32357-71PbPOnRvbArXKVTXhle1w-*-server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 14 Oct 2008 10:12:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [huub.van-dam{:}stfc.ac.uk] Hi Adam, Perhaps you could clarify a bit which sort of Hartree-Fock you are interested in: 1. Closed shell restricted Hartree-Fock (RHF) 2. Restricted open shell Hartree-Fock, typically high-spin, (ROHF) 3. All Hartree-Fock methods of spin restricted states, including low spin cases, (GRHF) 4. Unrestricted Hartree-Fock (UHF) 5. All of the above Maybe finding out where the biggest problems are is part of your initial investigation. This information would narrow the set of problems of interest down a bit. The other question is of course what do you consider small? Is an Iron atom sandwiched between two benzene rings still small or something like Fe4S8H4? Of course the smaller the better if want to test new approaches but what is practical will be limited by your resources. Anyway it will be interesting to see what list of molecules you'll end with. Best wishes, Huub ======================================================= Huub van Dam (huub.van-dam:_:stfc.ac.uk, +44-1925-603933) ======================================================= -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net] Sent: 14 October 2008 00:11 To: Vandam, Huub Subject: CCL: Small molecules with HF SCF convergence difficulty Sent to CCL by: Adam Hunter [spacyhunter#gmail.com] hi, all, I'm studying the SCF convergence problem. Can anybody provide me some small molecules which are hard to converge with the Hartree-Fock method? I know several such examples with DFT convergence difficulty, but have not found good examples for the Hartree-Fock method. Any help will be greatly appreciated. Thank you very much! all the best Adamhttp://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 Tue Oct 14 19:06:00 2008 From: "Adam Hunter spacyhunter{=}gmail.com" To: CCL Subject: CCL: Small molecules with HF SCF convergence difficulty Message-Id: <-37912-081014185828-5288-iSDXAwG9+Y3dcfOOjtc64Q||server.ccl.net> X-Original-From: Adam Hunter Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Oct 2008 15:58:04 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Hunter [spacyhunter^gmail.com] hi, Huub, Thank you for pointing out the ambiguity in my previous question. Here I want to clarify it as the following: 1. Any type of HF method is ok for me, say RHF, UHF, ROHF...... 2. Since now I'm doing coding on a PC, I can not deal with large system. To be honest, I don't know the upper limit size of the system which can be calculated with my old PC, but as the efficiency of testing and debugging is concerned, I think system with less than 50 electrons can be considered "small" in my sense. Thank you very much for your response. best wishes Adam Van Dam, HJJ (Huub) huub.van-dam::stfc.ac.uk wrote: > Sent to CCL by: "Van Dam, HJJ \(Huub\)" [huub.van-dam{:}stfc.ac.uk] > Hi Adam, > > Perhaps you could clarify a bit which sort of Hartree-Fock you are > interested in: > > 1. Closed shell restricted Hartree-Fock (RHF) > 2. Restricted open shell Hartree-Fock, > typically high-spin, (ROHF) > 3. All Hartree-Fock methods of spin restricted states, > including low spin cases, (GRHF) > 4. Unrestricted Hartree-Fock (UHF) > 5. All of the above > > Maybe finding out where the biggest problems are is part of your initial > investigation. This information would narrow the set of problems of > interest down a bit. > > The other question is of course what do you consider small? Is an Iron > atom sandwiched between two benzene rings still small or something like > Fe4S8H4? Of course the smaller the better if want to test new approaches > but what is practical will be limited by your resources. > > Anyway it will be interesting to see what list of molecules you'll end > with. > > Best wishes, > > Huub > > > ======================================================= > Huub van Dam (huub.van-dam^stfc.ac.uk, +44-1925-603933) > ======================================================= > > > -----Original Message----- > >> From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] >> > Sent: 14 October 2008 00:11 > To: Vandam, Huub > Subject: CCL: Small molecules with HF SCF convergence difficulty > > > Sent to CCL by: Adam Hunter [spacyhunter#gmail.com] hi, all, > I'm studying the SCF convergence problem. Can anybody provide me > some small molecules which are hard to converge with the Hartree-Fock > method? I know several such examples with DFT convergence difficulty, > but have not found good examples for the Hartree-Fock method. > Any help will be greatly appreciated. Thank you very much! > all the best > Adamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > >