[gmx-users] Re: Targeted MD

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jan 9 14:48:07 CET 2008

Stanislav Bobritsky wrote:
> *Ran Friedman wrote:*
> >Dear Stanislav,
> >
> >AFAIK there's no "targeted MD" in GMX. You can run EDS or use the
> >flooding algorithm.
> >
> >Ran.
> Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do targeted MD" in GMX.
Together with an explanation why one should not use it for proteins :-)

But I guess you know what you need.

When I read "targeted MD" I think about applying an external force in
order to reduce the RMSD between two structures, so that the dynamics
are somewhat perturbed, as it's done in CHARMM.


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