[gmx-users] essential dynamics

Bert de Groot bgroot at gwdg.de
Mon Aug 9 11:20:01 CEST 2004

John Simms wrote:
> Hi all,
> I would like to run essentail dynamics on a membrane protein, I have run an
> unconstrained simulation for 1ns and would like to use the eigenvectors for
> essential dynamics. I know that there is a program on the contibutions pages
> for the setup. So do i just make the ei file from this programs and use the
> command mdrun as normal ie
> mdrun -v -s full.tpr -o full.trr -e full.edr -ei full.edi -c
> after_full -nice X (without the grompp step)
> and the system will drive the simulation down the eigenvectors?

yes. The only thing is to create an appropriate "full.edi" file with the make_edi
tool. Please see my reply to Chris Shaw's question for details.


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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