[gmx-users] Targeted MD

Stanislav Bobritsky beavered at gmail.com
Wed Jan 9 13:41:46 CET 2008

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

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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