[gmx-users] Using user-tables for simulations in vacuum
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 16 16:08:04 CEST 2008
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
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> sapna sarupria wrote:
>
>
>
> ---------- Forwarded message ----------
> From: *sapna sarupria* <sapna.sarupria at gmail.com
> <mailto:sapna.sarupria at gmail.com>
> <mailto: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> <mailto: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 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.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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