[gmx-users] Targeted MD

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 9 13:59:58 CET 2008

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?

What's in your .mdp file?


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