[gmx-users] Simulation of a part of the system

X.Periole X.Periole at rug.nl
Thu Jun 16 08:53:11 CEST 2005

On Wed, 15 Jun 2005 19:19:05 -0300 (ART)
  Monique Brito <moniquebrito at yahoo.com.br> wrote:
> Hi people,
> In the middle of the protein I've working with
> there is a ligand.
> I intend to run a simulation with the whole
> protein, but only computing simulation of the
> ligand plus 20 angstrons around it; but without
> cutting off parts of the system. 
> Is it possible to do this in GROMACS?

Everything is possible ... You can selected yourself the
part of the protein you want to fix and then apply 
on it by defining position restrains (look for POSRES in
the manual). Or you can freeze it (look for f
I personaly prefer the position restrains. They still 
the "fixed" part to move around a position so that the
system is less constrained than by freezing.


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