sapna sarupria wrote:
Hello,
Thanks David for your response. Actually I have used the same tables for
simulations of the polymer in water and have had no problem with them.
Those simulations run for 4 ns without a problem. So the tables are
correct and I am sure of that. I am not using the CVS version and so I
give the energy and second derivative in the table. I have used
user-defined tables in the past and so the setup is correct in terms of
changing the mdp file and the top file. The problem seems to be more
system specific (meaning vacuum) than user error specific. Can you
suggest any other thing that may be the problem.
Have you checked energy components, temperature etc.?
Thanks a lot for your help.
Regards
Sapna
On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
sapna sarupria wrote:
---------- Forwarded message ----------
From: *sapna sarupria* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>
Date: Tue, Jul 15, 2008 at 9:16 AM
Subject: Using user-tables for simulations in vacuum
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
Hello users,
I am trying to do a simulation of a polymer chain (which is
simply a bead of unified methane molecules) in vacuum using
user-defined tables. The interactions are
Weeks-Chandler-Andersen instead of Lennard-Jones. However, when
I run the simulations, mdrun gives me a segmentation fault. When
I run simulations for the exact same configurations without the
tables (and therefore using VdW) the simulations run fine. In
addition, the starting configurations were obtained after 3ns
simulations of the polymer in water.
So I was wondering if there is any issue with using user-defined
tables with simulations in vacuum. If not do you have any idea
what could be going wrong.
Some details of the mdp file:
1. pbc is turned off.
2. there is no pressure coupling.
3. center of mass removal is set to angular.
4. temperature is 298 K and berendsen thermostat is used.
5. energy groups and table are defined (correctly).
6. the cut-offs are set to 1.0nm (box size is larger than 4 nm).
7. no constraints are being used.
Most obvious error source is the table itself. Do you use the CVS
version? In that case you should provide energy and force, otherwise
energy and second derivative. Distance units are in nm. Compare to
existing tables in share/gromacs/top
Thank you
Regards
Sapna
--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
------------------------------------------------------------------------
_______________________________________________
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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