[gmx-users] targeted molecular dynamics

[Berk Hess]

>Hi all,
>Is the targeted molecular dynamics algorithm implemented in the actual 
>version of GROMACS?
>Do I need additional software?
>Thanks in advance,
>Cheers,
>Ruben

I don't know what you mean exactly with "the" targeted molecular dynamics 
algorithm.
I think there are many algorithms which differ slightly.
I should warn you that in most cases targeted MD does NOT produce a reliable 
pathway
between two states.

In Gromacs there are several ways to force a simulation in a certain 
direction.
One is the pull code, where you can pull on the center of mass of two, or 
more,
groups.
As of version 3.2 the position restraint coordinates (and forces) can be 
interpolated
between two states with the free energy parameter coupling method. This can 
be used
to force (part of) the system from one conformation to another. Use grompp 
-h to see
how to supply the two conformations.

Berk.

_________________________________________________________________
MSN Search, for accurate results! http://search.msn.nl