From owner-chemistry@ccl.net Tue Sep 25 00:23:00 2007 From: "chenzhz[]sohu.com" To: CCL Subject: CCL: formulate flexible weakly bound complexes by Boltzmann factor Message-Id: <-35245-070924223214-31632-gu7g1hgt+uOKLCJ49kwThg=server.ccl.net> X-Original-From: Content-Type: multipart/related; boundary="----=_Part_113_30844660.1190685140550" Date: Tue, 25 Sep 2007 09:52:20 +0800 (CST) Mime-Version: 1.0 Sent to CCL by: [chenzhz#,#sohu.com] ------=_Part_113_30844660.1190685140550 Content-Type: multipart/alternative; boundary="----=_Part_112_11531367.1190685140549" ------=_Part_112_11531367.1190685140549 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit
Dear CCLers:                                                                                                                                                                                                                                                                                                                                         &nbs p;                                   
there are two flexible molecules A and B. They form through their intermolecular interactions flexible complexes:
        A
        |
A-B, B and B-A,  implying that these complexes have different entropic changes.
Then,the Boltzmann factor for the respective complexes is represented by
   P(i)=exp(-Har(i)/kT)/Q .

My question is:
i)how to determine the representation of Har(i) in Monte Carlo simulation? in the simulation the interaction energy obtained by MM is not equivelent to Har(i).  Did we have to take entropic effects in the complex into account? To say, Har(i) is replaced with Gibbs free energy de ltaG. Are there any literatures?
ii)are there any arithmatic methods in literature or internet?

Any help will be much appreciated.
Chen
------=_Part_112_11531367.1190685140549 Content-Type: text/html Content-Transfer-Encoding: 8bit
Dear CCLers:                                                                                                                                                              & nbsp;                                                                                                                                                                      ;                                        
there are two flexible molecules A and B. They form through their intermolecular interactions flexible complexes:
        A
        |
A-B, B and B-A,  implying that these complexes have different entropic changes.
Then,the Boltzmann factor for the respective complexes is represented by
   P(i)=exp(-Har(i)/kT)/Q .

My question is:
i)how to determine the representation of Har(i) in Monte Carlo simulation? in the simulation the interaction energy obtained by MM is not equivelent to Har(i).  Did we have to take entropic effects in the complex into account? To say, Har(i) is repla ced with Gibbs free energy deltaG. Are there any literatures?
ii)are there any arithmatic methods in literature or internet?

Any help will be much appreciated.
Chen


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------=_Part_112_11531367.1190685140549-- ------=_Part_113_30844660.1190685140550-- From owner-chemistry@ccl.net Tue Sep 25 06:34:01 2007 From: "Daniel Jana dfjana###gmail.com" To: CCL Subject: CCL:G: g03 Message-Id: <-35246-070925053514-25924-9H+ZykMBpG7DtUHWWywTuw*o*server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Sep 2007 10:35:12 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana---gmail.com] Hello! hadi H H hwchems]~[yahoo.com wrote: > The problem is the maximum size for each file under linux in my pc is 2 GB and the scratch files for the calculations need more space. > I am using %RWF=/scratch/1,1GB,/scratch/2,100MW,...... and it works for some calculations, and not for all. > So please, my question is: > How can I make the maximum file size under linux unlimitted? > The problem with the 2 GB maximum file size was solved in the C01 revision of Gaussian03 so I'd guess you are using an older version. Anyway, for the 32 bit architecture, there is a limit of 16 GB (even for the revisions after C01. This is an inherent problem of the 32 bits and not of Gaussian03). > Can I split the scratch files to many files with limit size? > Yes, you can! It's similar to the principle you were using but instead of files (as it appears to be what you are giving with the 1 and 2 up there) you have to give folders. So what you should have given the program is something like: %RWF=/scratch/1/,1GB,/scratch/2/,100MW,... Since you have up to 2 GB giving 100 MW (800 MB) is a small value. You should put something like 1900MB or something like it. More info on this here: http://www.gaussian.com/g_ur/m_running.htm Release notes for Gaussian (where I checked the 2 GB limit problem) here: http://www.gaussian.com/g_tech/g03_rel.htm Best luck with your problem, Daniel Jana > Can you kindly advise me?? > > From owner-chemistry@ccl.net Tue Sep 25 08:37:01 2007 From: "Fay al Allouti faycal.allouti#aci.uni-heidelberg.de" To: CCL Subject: CCL:G: ADMP restrictions in gaussian Message-Id: <-35247-070925051527-24507-DgO5EvwhqLcQx0gI6Pa8xw(_)server.ccl.net> X-Original-From: "Fay al Allouti" Date: Tue, 25 Sep 2007 05:15:23 -0400 Sent to CCL by: "Fay al Allouti" [faycal.allouti|-|aci.uni-heidelberg.de] Hello, I'm was trying to perform an ADMP calculation with Gaussian and I faced a first problem. The job crashes just after reading the molecular geometry with the message : "Allocation error in SaveZR." I found non mention of the this in any webpage so, as a complet newby, I wanted to ask if some ADMP specialist could help me with this. I'm also wandering if there are any limitations in the use of ADMP like for example to certain functionals and basis sets. I'm using an ECP on one of the atoms in my system. In advance, I thank you for your help. Dr. Fayal Allouti Anorganisch-Chemisches Institut der Universitt Heidelberg Im Neuenheimer Feld 270. D-69120 Heidelberg Tel.: (+49) 6221 54 8649 Fax.: (+49) 6221 54 4197 e-mail: faycal.allouti|a|aci.uni-heidelberg.de From owner-chemistry@ccl.net Tue Sep 25 11:47:01 2007 From: "ShanshanQin Qin sansanqin00[-]mails.tsinghua.edu.cn" To: CCL Subject: CCL: About towhee Message-Id: <-35248-070925103230-23280-EV16zmG/JrE6hstG/BVXJA-*-server.ccl.net> X-Original-From: "ShanshanQin Qin" Date: Tue, 25 Sep 2007 10:32:26 -0400 Sent to CCL by: "ShanshanQin Qin" [sansanqin00|,|mails.tsinghua.edu.cn] Is there anyone familiar with towhee? I installed it like this: Here is the process of configuration: [root*|*th218110 towhee-5.2.2] ./configure --prefix=/usr/local/towhee checking whether to enable maintainer-specific portions of Makefiles... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets (MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... f95 checking whether we are using the GNU Fortran 77 compiler... yes checking whether f95 accepts -g... yes checking how to get verbose linking output from f95... -v checking for Fortran libraries of f95... -L/usr/lib/gcc/i386-redhat-linux/4.1.0 -L/usr/lib/gcc/i386-redhat-linux/4.1.0/../../.. -lgfortranbegin -lgfortran -lm -lgcc_s checking for strstr... yes configure: creating ./config.status .................. .................. Here is my installation: [root*|*th218110 Source] make install make[1]: Entering directory `/usr/local/towhee-5.2.2/Source' /bin/sh ../install/mkinstalldirs /usr/local/towhee/bin mkdir -p -- /usr/local/towhee/bin /usr/bin/install -c towhee /usr/local/towhee/bin/towhee /usr/bin/install -c forcefield /usr/local/towhee/bin/forcefield /usr/bin/install -c fitcoex /usr/local/towhee/bin/fitcoex make[1]: Nothing to be done for `install-data-am'. make[1]: Leaving directory `/usr/local/towhee-5.2.2/Source' However after installation there are only 3 programms in the /usr/local/towhee/bin directory:fitcox forcefield towhee Is this normal? If not what's wrong with my installation process? How many programms should be there if I install it correctly? Any suggestion will be appreciated, thanks very much in advance. From owner-chemistry@ccl.net Tue Sep 25 12:21:01 2007 From: "Richard Leo Wood woodx278~~umn.edu" To: CCL Subject: CCL: DFTB geometries Message-Id: <-35249-070925120545-14618-03zkX02sCN/U2QN1GCvfuw[]server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Tue, 25 Sep 2007 12:05:42 -0400 Sent to CCL by: "Richard Leo Wood" [woodx278!A!umn.edu] Hi all, I'm encountering a problem with geometries obtained using DFTB and I am wondering if anyone else has encountered a similar problem. I have a series of 12 molecules that I am using to do a validation study. All of the molcules contian nitrogen and seven of them contain nitrogen and sulfur, as well as carbon, hydrogen and oxygen. The problem I am having is that for all seven of the sulfur containing molecules, I get weird geometries, if they even converge (two of the seven won't even converge). What I mean by weird is that some of the bond lengths are REALLY long (like C-C bond of 4 Angstroms or more). I'm wondering if anyone else has encountered this "problem" using DFTB and if there is perhaps a work-around to it. TIA, Richard From owner-chemistry@ccl.net Tue Sep 25 15:56:01 2007 From: "Ben King king:-:chem.unr.edu" To: CCL Subject: CCL:G: Relaxed PES in g03 using forcefield? Message-Id: <-35250-070925142951-20748-HkNPfj+JV76uW+gZNip/ew]~[server.ccl.net> X-Original-From: Ben King Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 25 Sep 2007 10:23:33 -0700 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Ben King [king^chem.unr.edu] Dear CCLers: Summary: how can one use gaussian to perform a relaxed potential energy scan with a force field? We need to generate a 2-D potential energy surface for a bond- breaking coupled with a torsion. Gaussian's tools for performing a relaxed PES using the modredundant option to opt are ideal, but Z- matrix tools could also work. Here is the problem: Gaussian (g03) completely ignores any constraints when we use molecular mechanics (amber, uff, etc.), using either Z-matrices or opt=modredundant. This also happens in OMION methods using a MM fragment. Our syntax is correct, as we do these same calculations (albeit inaccurately and only over limited portions of the PES) using semi-empirical methods. We must use a molecular mechanics force field: van der Waals interaction are important in our molecule and we need to study the portion of the bond dissociation region that is poorly described by single references wavefunctions (e.g., C-C bond distances of 1.4 A to 6.0 A in 0.2 A increments). The molecule is large (C62H38), so high- level ab initio methods are prohibitively time consuming. Molecular mechanics will give us the most realistic description of the molecular behavior, provided that we use a Morse potential for the bond dissociation. If anyone can suggest a procedure to generate a PES from a force field, I would be grateful. This is one of those irritating things that should be easy but ends up being exceptionally difficult. Also, if anyone knows why Gaussian behaves so oddly with MM methods, I would be delighted to know. Thanks, Ben p.s. The version of Gaussian is: Gaussian 03: AM64L-G03RevC.02 12- Jun-2004 p.p.s. We are limping through this by running thousands of individual constrained optimizations using Tinker, but it isn't pretty... ---- Benjamin T. King, Associate Professor Department of Chemistry/216 University of Nevada, Reno 89557 tel (775) 784-1736 fax (775) 784-6804 king-.-chem.unr.edu http://www.chem.unr.edu/faculty/btk/ From owner-chemistry@ccl.net Tue Sep 25 16:31:00 2007 From: "jim li g_p_li__yahoo.com" To: CCL Subject: CCL: display charge density and local potential of VASP calculations Message-Id: <-35251-070925141114-19068-d3jRwebDKMPwr3DYJMgDWQ~!~server.ccl.net> X-Original-From: jim li Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1979358434-1190740264=:20300" Date: Tue, 25 Sep 2007 10:11:04 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: jim li [g_p_li**yahoo.com] --0-1979358434-1190740264=:20300 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello: I use VASP to do the calculations. I am looking for a graphics program to display VASP charge density, local potential, geometric structure, band structure, density of states, geometry and electron density, and local potential and geometry together. Any help is appreciated. Jim --------------------------------- Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. --0-1979358434-1190740264=:20300 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello:
 
I use VASP to do the calculations.
I am looking for a graphics program to display VASP charge density, local potential, geometric structure, band structure, density of states, geometry and electron density,  and local potential and geometry together.
Any help is appreciated.
 
Jim

Moody friends. Drama queens. Your life? Nope! - their life, your story.
Play Sims Stories at Yahoo! Games. --0-1979358434-1190740264=:20300-- From owner-chemistry@ccl.net Tue Sep 25 17:06:00 2007 From: "Alexandre Hocquet alexandre.hocquet,,ensic.inpl-nancy.fr" To: CCL Subject: CCL: Journes d'Histoire de la Chimie/History of Chemistry Event Message-Id: <-35252-070925130638-30157-vcTZEDKhWLqd55fr9YW1UQ|,|server.ccl.net> X-Original-From: "Alexandre Hocquet" Date: Tue, 25 Sep 2007 13:06:34 -0400 Sent to CCL by: "Alexandre Hocquet" [alexandre.hocquet],[ensic.inpl-nancy.fr] dear CClers, My apologies for posting in French. Basicaly, on September the 26th and 27th will be held in Nancy two "History of Chemistry days". The second day is about history of theoretical chemistry and one of the talks wil be dedicated to the CCl and its revered administrator : Jan Labanowski. Les mercredi et jeudi 26 et 27 septembre prochains auront lieu les Journes d'Histoire de la Chimie organises par le Club d'Histoire de la Chimie de la Socit Franaise de Chimie. Elles se tiennent l'Acadmie de Stanislas (43 rue Stanislas) et l'entre est libre. Cette anne les thmes retenus sont la chimie Nancy (mercredi) et l'histoire de la chimie thorique (jeudi). Vous pouvez consulter le programme dtaill sur : http://www.sfc.fr/GrHist/Grhist.htm puis cliquer sur la rubrique Manifestations ou bien directement sur : http://www.sfc.fr/GrHist/NancySept07.pdf Yours, Alexandre Hocquet