sapna sarupria wrote:
---------- Forwarded message ----------
From: *sapna sarupria* <[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]>>
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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