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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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
************************************************
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