[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>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.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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