[gmx-users] Using user-tables for simulations in vacuum
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 18 09:20:25 CEST 2008
sapna sarupria wrote:
> Hello,
>
> The simulation does not run even for one step and therefore, it is not
> possible for me to check any of the components such as energy,
> temperature etc. There is no error message except for "segmentation
> fault". It does the same thing if I try to energy minimize the system
> instead of running an MD simulation. The corresponding mdp file is
> pasted below:
> cpp = /lib/cpp
> constraints = none
> integrator = steep
> nstcgsteep = 500
> emtol = 500.0
> emstep = 0.001
> vdwtype = user
> energygrps = POL
> energygrp_table = POL POL
>
> The commands I use are as follows:
> grompp -f em.mdp -p 25mer_wca_vac.top -c 3.5ns.gro
> mdrun -s topol.tpr -table table.xvg
>
Maybe you should make the table way longer. IIRC this is in vacuum with
no cutoffs. Then the interactions should still fall within the length of
the table.
> Regards
> Sapna
>
>
> On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> 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>
> <mailto: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>>
> <mailto: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>> <mailto: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>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> spoel at gromacs.org <mailto:spoel at gromacs.org>
> <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
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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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>
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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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>
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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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