[gmx-users] Using user-tables for simulations in vacuum

sapna sarupria sapna.sarupria at gmail.com
Wed Jul 16 13:01:30 CEST 2008

---------- Forwarded message ----------
From: sapna sarupria <sapna.sarupria at gmail.com>
Date: Tue, Jul 15, 2008 at 9:16 AM
Subject: Using user-tables for simulations in vacuum
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

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
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.

Thank you


Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
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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