[gmx-users] Steered MD

Mike M nmr.mike.nmr at gmail.com
Mon Jun 4 11:53:30 CEST 2012

Dear Gromacs Users,

I am trying to study the conformational path from state A to state B with
targeted molecular dynamics. These two states are two different structures
of a peptide that I have calculated after a series of nmr experiments. I
have perform 100ns simulations separately of the two peptides to assess
their stabilty over the course of the simulations, but now I wonder how can
I direct my system A towards the state named as B. In the manual I have
read what it is said in the manual about this topic and the usage of -rb to
provide the coordinates of the B state, but I did not find out how to
properly set the simulation.

Has anyone done this before?

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