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

sapna sarupria sapna.sarupria at gmail.com
Wed Jul 16 18:03:53 CEST 2008


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

Regards
Sapna


On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel <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>> 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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>>
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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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>



-- 
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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