Dear Stanislav, AFAIK there's no "targeted MD" in GMX. You can run EDS or use the flooding algorithm.
Ran. Stanislav Bobritsky wrote: > Hello dear gromacs users! > I`m trying to do targeted MD. I have two protein conformations which > are different from each other by one loop position. I need to force > conformation A to B. > It was following commands executed: > > grompp -с box.gro -f md.mdp -r conf1.pdb -rb conf2.pdb -p topol.top -o > transformer.tpr > > mdrun -s transformer.tpr -o -x -c -e -g -v > > But it can be viewed from traj.xtc that conformation didn`t change. > Protein just spins (with speed increasing), and desired loop does not > move. > > What can I do to fix it? > > Best regards, Stanislav Bobritsky, > > ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine. > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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