[gmx-users] Targeted MD

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jan 9 14:01:52 CET 2008

Dear Stanislav,

AFAIK there's no "targeted MD" in GMX. You can run EDS or use the
flooding algorithm.


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.
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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: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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