From owner-chemistry@ccl.net Wed Dec 28 10:47:00 2005 From: "Richard Leo Wood rwoodphd**yahoo.com" To: CCL Subject: CCL: FEP simulation set up Message-Id: <-30402-051228095313-16512-DbkfCvGELU+8KEzi7UlWSQ##server.ccl.net> X-Original-From: "Richard Leo Wood" Sent to CCL by: "Richard Leo Wood" [rwoodphd#yahoo.com] Hi all, I've posted the following question to the NAMD list and have yet to get a reply. I'm trying to set up an FEP calculation to be run in NAMD for a hexasaccharide going to a pentasaccharide. I've got the coordinates for the hexasaccharide and I know which atoms have to "vanish", but I am having difficulty generating a psf file (and a topology?) for the calculation. I've "marked" the atoms in my pdb file which I want to "go away" and I've added a hydrogen which wants to appear. The problem lies in my topology file, I believe, but I'm not sure how to set it up. Basically, I've got 6 sugar residues and five patches versus 5 residies and four patches. How does one set this up so one gets the correct topology to give the correct psf? It's obvioulsly more complicated than just adding a hydrogen to the pdb file. On the other hand, a sugar ring is being replaced by a hydrogen. TIA, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd[-]yahoo.com From owner-chemistry@ccl.net Wed Dec 28 11:22:00 2005 From: "Sue L chsue2004::yahoo.com" To: CCL Subject: CCL:G: CPCM calculation in Gaussian 03 Message-Id: <-30403-051228070220-6392-Syki4vbhKk85DmoW2h2ghQ..server.ccl.net> X-Original-From: "Sue L" Sent to CCL by: "Sue L" [chsue2004:+:yahoo.com] I have run a CPCM calculation in G03 for a molecule (812 basis function) using CH3CN as a solvent. However, the calculations are stuck in a l302 process for a very long time. Do anyone know how to solve the problem? Thanks a lot. Sue From owner-chemistry@ccl.net Wed Dec 28 11:57:00 2005 From: "Aggelos Avramopoulos aggavramop[-]yahoo.gr" To: CCL Subject: CCL:G: =?iso-8859-7?q?=C8=DD=EC=E1:=20CCL:=20sum=20over=20states?= Message-Id: <-30404-051228095649-16832-0VWsJTv4lzsK8bcFsMsvJA(-)server.ccl.net> X-Original-From: Aggelos Avramopoulos Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1641089527-1135778200=:26252" Date: Wed, 28 Dec 2005 13:56:40 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Aggelos Avramopoulos [aggavramop**yahoo.gr] --0-1641089527-1135778200=:26252 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 8bit Hi In order to compute the the first polarizability you have to consider the trasition dipole moment matrix elements; these can be computed under the CIS method as it is implement in G98 or G03. However CIS method can not quantitatively describe the results but often show the correct trend and give qualitatively correct results. Moreover results depend from the selected excited states unless there is a well defined electronic transition. . The advantage of the SOS is that it matches the traditional interpretation of NLO phenomena using intermediate excited states The above written are valid for the case of the hyperpolarizabilities. In these cases the value of a property can be computed under the two state model for beta (see JACS 114, 10338 (92), JCP 1171649 (02), JACS 127,10977(05) and under the the so-called three state model approximation for gamma (see J. F. Orr and J. F. Ward, Mol. Phys., 20, 513 (1971). A. Shuai and J. L. Bredas, Phys. Rev. B, 46, 4395 (1992). M. G. Kuzyk, C. W. Dirk, Phys. Rev. A., 41, 5098 (1990) C. W. Dirk, L-Tak Cheng, M. G. Kuzyk, Int. J. Quant. Chem., 43, 27 (1992).) The best Dr Aggelos Avramopoulos "liaoyi..u.washington.edu" έγραψε: Sent to CCL by: liaoyi*u.washington.edu Hi, there: A new bee want to try some calculations of first and 2nd order hyperpolarizability using sum over states method. Could anybody give some guide about the papers and softwares about that? Many thanks. yihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr --0-1641089527-1135778200=:26252 Content-Type: text/html; charset=iso-8859-7 Content-Transfer-Encoding: 8bit
Hi
In order to compute the the first polarizability you have to consider the
trasition dipole moment matrix elements; these can be computed under the
CIS method as it is implement in G98 or G03. However CIS method can not quantitatively describe the results but often show the correct trend and give
qualitatively correct results. Moreover results depend from the selected excited states unless there is a well defined electronic transition. . The advantage of the SOS is that it matches the traditional interpretation of NLO phenomena using intermediate excited states
The above written are valid for the case of the hyperpolarizabilities. In these cases the value of a property can be computed under the two state model for beta (see JACS 114, 10338 (92), JCP 1171649 (02), JACS 127,10977(05) and under the the so-called three state model approximation for gamma (see
 
  1. J. F. Orr and J. F. Ward, Mol. Phys., 20, 513 (1971).
  2. A. Shuai and J. L. Bredas, Phys. Rev. B, 46, 4395 (1992).
  3. M. G. Kuzyk, C. W. Dirk, Phys. Rev. A., 41, 5098 (1990)
  4. C. W. Dirk, L-Tak Cheng, M. G. Kuzyk, Int. J. Quant. Chem., 43, 27 (1992).)
The best 
Dr Aggelos Avramopoulos 
"liaoyi..u.washington.edu" <owner-chemistry(!)ccl.net> έγραψε:
Sent to CCL by: liaoyi*u.washington.edu
Hi, there:
A new bee want to try some calculations of first and 2nd order hyperpolarizability using sum over states method. Could anybody give some guide about the papers and softwares about that?
Many thanks.
yi


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Χρησιμοποιείτε Yahoo!
Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων
http://login.yahoo.com/config/mail?.intl=gr --0-1641089527-1135778200=:26252-- From owner-chemistry@ccl.net Wed Dec 28 19:29:01 2005 From: "david.giesen^^^kodak.com" To: CCL Subject: CCL:G: Some problem with running Linda7.1 in gaussian03 Message-Id: <-30405-051228153235-4279-fSfG2QvFy/lvDJnqLzkWdA,server.ccl.net> X-Original-From: david.giesen],[kodak.com Content-Type: text/plain; charset="US-ASCII" Date: Wed, 28 Dec 2005 14:21:19 -0500 MIME-Version: 1.0 Sent to CCL by: david.giesen^^kodak.com Does the job run properly in serial mode? If so, then my first guess is that you might need to change the value of SHMMAX in /proc/sys/kernel/shmmax to something larger, like 268435456 (256 Mb). Dave Giesen "Qui Chun Lee s4553711===yahoo.com.tw" Sent by: owner-chemistry~!~ccl.net 12/21/2005 03:01 AM Please respond to "CCL Subscribers" To "Giesen, David J " cc Subject CCL:G: Some problem with running Linda7.1 in gaussian03 Sent to CCL by: "Qui Chun Lee" [s4553711.~!~.yahoo.com.tw] I have a cluster and want to use Linda running parallel working. Now I test a input file test.gjf as below: ============ %mem=15MW %NProcLinda=2 %chk=water.chk HF/6-31g(d,p) OPT opt 0 1 H O 1 r1 H 2 r1 1 a1 r1=1.0 a1=104.5 ============ and running in the command %g03l < test.gjf , some problem appear. So I set -vv to show more information , and the result as below .I guess there are some setting not correct but I don't know where to adjust setting well.My another thinking is not to run work on cluster1(my master) ,can it be worked and how to do this? Is there any suggest to solve this problem ? Thanks a lot. PS.cluster1.private.net(192.168.0.101) <=== my master in cluster node1.private.net(192.168.0.102) <=== node2.private.net(192.168.0.103) <===another 2 slave nodes OS:Fedora Core3 Log files: setenv GAUSS_EXEDIR /pub/g03/linda-exe:/pub/g03/bsd:/pub/g03/private:/pub/g03 echo /pub/g03/linda-exe:/pub/g03/bsd:/pub/g03/private:/pub/g03 /pub/g03/linda-exe:/pub/g03/bsd:/pub/g03/private:/pub/g03 g03 Entering Gaussian System, Link 0=g03 Initial command: /pub/g03/l1.exe /home/user/g03test/Gau-6343.inp -scrdir=/home/user/g03test/ Entering Link 1 = /pub/g03/l1.exe PID= 6344. From owner-chemistry@ccl.net Wed Dec 28 20:04:01 2005 From: "Spencer Ericksen spencer_ericksen a hotmail.com" To: CCL Subject: CCL: FEP simulation set up Message-Id: <-30406-051228161816-10079-5bqaEKrINxDhzYpnRCYTgg!^!server.ccl.net> X-Original-From: "Spencer Ericksen" Content-Type: text/plain; format=flowed Date: Wed, 28 Dec 2005 21:18:10 +0000 Mime-Version: 1.0 Sent to CCL by: "Spencer Ericksen" [spencer_ericksen,+,hotmail.com] I just starting using NAMD so I wouldn't be of much help. However, have you subscribed to the NAMD -l mailing list? You may submit your questions there. Mailing list for users of NAMD: http://www.ks.uiuc.edu/Research/namd/ Spencer S. Ericksen, Ph.D. 420 W. Wilson St. Apt. 108 Madison, WI 53703 304-685-7660 ----Original Message Follows---- > From: "Richard Leo Wood rwoodphd**yahoo.com" Reply-To: "CCL Subscribers" To: "Ericksen, Spencer " Subject: CCL: FEP simulation set up Date: Wed, 28 Dec 2005 11:13:48 -0500 Received: from server.ccl.net ([66.93.212.15]) by bay0-mc10-f3.bay0.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Wed, 28 Dec 2005 08:34:13 -0800 Received: from server.ccl.net (ccl [127.0.0.1])by server.ccl.net (8.13.1/8.13.1) with ESMTP id jBSGEvvB014659for ; Wed, 28 Dec 2005 11:34:12 -0500 Received: (from root_-_localhost)by server.ccl.net (8.13.1/8.13.1/Submit) id jBSGDm2x013767for spencer_ericksen_-_hotmail.com; Wed, 28 Dec 2005 11:13:48 -0500 X-Message-Info: JGTYoYF78jHUc4abfG/GpdWHrXBzeZG9Gh2FtoKHEkg= X-Original-From: "Richard Leo Wood" X-Preference-Score: 0 X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Return-Path: owner-chemistry_-_ccl.net X-OriginalArrivalTime: 28 Dec 2005 16:34:13.0281 (UTC) FILETIME=[89629110:01C60BCC] Sent to CCL by: "Richard Leo Wood" [rwoodphd#yahoo.com] Hi all, I've posted the following question to the NAMD list and have yet to get a reply. I'm trying to set up an FEP calculation to be run in NAMD for a hexasaccharide going to a pentasaccharide. I've got the coordinates for the hexasaccharide and I know which atoms have to "vanish", but I am having difficulty generating a psf file (and a topology?) for the calculation. I've "marked" the atoms in my pdb file which I want to "go away" and I've added a hydrogen which wants to appear. The problem lies in my topology file, I believe, but I'm not sure how to set it up. Basically, I've got 6 sugar residues and five patches versus 5 residies and four patches. How does one set this up so one gets the correct topology to give the correct psf? It's obvioulsly more complicated than just adding a hydrogen to the pdb file. On the other hand, a sugar ring is being replaced by a hydrogen. TIA, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd]![yahoo.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt