[gmx-users] Steered MD

Miguel Ángel Mompeán García mig.mompean at gmail.com
Tue Jun 5 13:37:22 CEST 2012

You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
implemented in GROMACS (hope anyone corrects me if I am wrong)

2012/6/4 Mike M <nmr.mike.nmr at gmail.com>

> 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?
> Thanks,
> Mike
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