[gmx-users] How to specify .mdp file for position restrained simulation?
jantonioms J. A. Mondragon S
jantonioms at gmail.com
Tue Nov 20 14:24:14 CET 2007
you need to run genpr to generate a restrained position file
posresfile.itp with a determined force constant value fc and include
the name file in *.mdp file using define label, for example, run
genpr -f my_molecule.pdb -o posresfile.itp -fc 20
edit *.mdp to include
cpp = /usr/bin/cpp
On Nov 20, 2007 7:30 AM, Peggy Yao <peggy.yao at gmail.com> wrote:
> How to specify the .mdp file in order to run position restrained
> simulation? From the examples I found on the internet, it seems that
> the only difference between the .mdp file for position restrained
> simulation and the one for actual MD simulation is the simulation time
> -- the position restrained simulation is much shorter. Is this
> observation true in general?
> If yes, usually, how long is enough for the position restrained simulation?
> If not, how to specify the .mdp file for position restrained simulation then?
> Thanks a lot!
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users