[gmx-users] How to use g_energy after parellal mdrun

[Jochen Hub]

vivek sharma wrote:
> Hi Jochen,
>
> Thanks for your response. That was some syntax error, now I am getting 
> only single .edr file.
> Is there any restriction in mdp file parameters while running it in 
> parallel mode ?
> And, is it necessary to run energy minimization and position 
> restraining before running final mdrun ?
>
Yes, always run an EM before MD. And it is highly recommended to run a 
PR too, to allow the water shell and the protein to relax without 
inducing some initial artifacts on the protein. During PR, check if the 
potential and the box vectors seem converged (g_energy). If not extend 
the PR.

Best, Jochen

> With Thanks,
> Vivek
>
> 2008/8/27 Jochen Hub <jhub at gwdg.de <mailto:jhub at gwdg.de>>
>
>     vivek sharma wrote:
>
>         Hi There,
>         I am running gromacs in a parellel architecture using -np 20.
>         Now I want to generate the energy plot using g_energy, but
>         there are 20 .edr files.
>
>     Really? I get only one ener.edr, even in parallel mode. Or did you
>     use -multi?
>
>     Jochen
>
>
>
>
>         How should I use the g_energy command or which .edr file I
>         should use?
>
>         Any suggestion would be of great help..
>
>         With Thanks,
>         Vivek
>         ------------------------------------------------------------------------
>
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>     -- 
>     ************************************************
>     Dr. Jochen Hub
>     Max Planck Institute for Biophysical Chemistry
>     Computational biomolecular dynamics group
>     Am Fassberg 11
>     D-37077 Goettingen, Germany
>     Email: jhub[at]gwdg.de <http://gwdg.de>
>     Tel.: +49 (0)551 201-2312
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************