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 . . . define= -DPOSRESFILE On Nov 20, 2007 7:30 AM, Peggy Yao <[EMAIL PROTECTED]> wrote: > Hi, > > 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! > > Peggy > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
