[gmx-users] targeted molecular dynamics

Berk Hess gmx3 at hotmail.com
Tue Mar 23 16:05:01 CET 2004

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

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

In Gromacs there are several ways to force a simulation in a certain 
One is the pull code, where you can pull on the center of mass of two, or 
As of version 3.2 the position restraint coordinates (and forces) can be 
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.


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