[gmx-users] essential dynamics

[Bert de Groot]

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.

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________