[gmx-users] Using user-tables for simulations in vacuum
sapna.sarupria at gmail.com
Wed Jul 16 15:54:01 CEST 2008
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
Thanks a lot for your help.
On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> sapna sarupria wrote:
>> ---------- Forwarded message ----------
>> From: *sapna sarupria* <sapna.sarupria at gmail.com <mailto:
>> 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 <mailto:
>> 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.
> 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
> 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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> 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.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
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