From owner-chemistry@ccl.net Wed Dec 28 10:47:00 2005
From: "Richard Leo Wood rwoodphd**yahoo.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: FEP simulation set up
Message-Id: <-30402-051228095313-16512-DbkfCvGELU+8KEzi7UlWSQ##server.ccl.net>
X-Original-From: "Richard Leo Wood" <rwoodphd]|[yahoo.com>
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" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: CPCM calculation in Gaussian 03
Message-Id: <-30403-051228070220-6392-Syki4vbhKk85DmoW2h2ghQ..server.ccl.net>
X-Original-From: "Sue L" <chsue2004||yahoo.com>
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" <owner-chemistry(-)server.ccl.net>
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 <aggavramop(a)yahoo.gr>
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Sent to CCL by: Aggelos Avramopoulos [aggavramop**yahoo.gr]
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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" <owner-chemistry(!)ccl.net> ������:
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---------------------------------
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<DIV>Hi</DIV> <DIV>In order to compute the the first polarizability you have to consider the </DIV> <DIV>trasition dipole moment matrix elements; these can be computed under the </DIV> <DIV>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 </DIV> <DIV>qualitatively correct results. Moreover results depend from the selected excited states unless there is a well defined electronic transition. <SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">. The advantage of the SOS is that it matches the traditional interpretation of NLO phenomena using intermediate excited states </SPAN></DIV> <DIV>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 <SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">the so-called three state model approximation for gamma (see </SPAN></DIV> <DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA"></SPAN><FONT face="Times New Roman" size=3> </DIV> <OL style="MARGIN-TOP: 0in" type=1> <LI class=MsoNormal style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2">J. F. Orr and J. F. Ward, <I>Mol. Phys., </I><B>20, </B>513 (1971).</LI> <LI class=MsoNormal style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2">A. Shuai and J. L. Bredas, <I>Phys. Rev. B</I>, <B>46, </B>4395 (1992).</LI> <LI class=MsoNormal
style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2"><SPAN lang=DE style="mso-ansi-language: DE">M. G. Kuzyk, C. W. Dirk, <I>Phys. Rev. A., </I><B>41, </B>5098 (1990)</SPAN></FONT><SPAN lang=DE style="mso-ansi-language: DE"></SPAN></LI> <LI class=MsoNormal style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2"><SPAN lang=DE style="mso-ansi-language: DE">C. W. Dirk, L-Tak Cheng, M. G. Kuzyk, <I>Int. J. Quant. Chem., </I><B>43, </B>27 (1992).) </SPAN><BR></LI></OL> <div class=MsoNormal style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2">The best </div> <div class=MsoNormal style="TEXT-ALIGN: justify; tab-stops: list .5in; mso-list: l0 level1 lfo2">Dr Aggelos Avramopoulos <BR><B><I>"liaoyi..u.washington.edu" <owner-chemistry(!)ccl.net></I></B> ������:</div> <BLOCKQUOTE class=replbq style="BORDER-LEFT: #1010ff 2px solid; MARGIN-LEFT: 5px; PADDING-LEFT: 5px">Sent to CCL by:
liaoyi*u.washington.edu<BR>Hi, there:<BR>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?<BR>Many thanks.<BR>yi<BR><BR><BR><BR<BR<BR<BR<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/chemistry/sub_unsub.shtml<BR><BR<BR><BR<BR><BR<BR><BR<BR>http://www.ccl.net/spammers.txt<BR><BR<BR><BR<BR><BR><BR><BR></BLOCKQUOTE><BR> <DIV></DIV><p>
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From owner-chemistry@ccl.net Wed Dec 28 19:29:01 2005
From: "david.giesen^^^kodak.com" <owner-chemistry,server.ccl.net>
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" <owner-chemistry~!~ccl.net>
Sent by: owner-chemistry~!~ccl.net
12/21/2005 03:01 AM
Please respond to
"CCL Subscribers" <chemistry~!~ccl.net>
To
"Giesen, David J " <david.giesen~!~kodak.com>
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" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: FEP simulation set up
Message-Id: <-30406-051228161816-10079-5bqaEKrINxDhzYpnRCYTgg!^!server.ccl.net>
X-Original-From: "Spencer Ericksen" <spencer_ericksen]~[hotmail.com>
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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" <owner-chemistry_-_ccl.net>
Reply-To: "CCL Subscribers" <chemistry_-_ccl.net>
To: "Ericksen, Spencer " <spencer_ericksen_-_hotmail.com>
Subject: CCL: FEP simulation set up
Date: Wed, 28 Dec 2005 11:13:48 -0500
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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