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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 16 15:23:58 CEST 2008

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 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	spoel at gromacs.org   http://folding.bmc.uu.se

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