[gmx-users] MD localized in the active site

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 17 21:01:16 CET 2010

Anna Marabotti wrote:
> Dear gmx-users,
> I'd like to perform a molecular dynamics simulation on a protein-ligand 
> complex, in such a way that only residues belonging to the active 
> site can move, whereas the rest of the protein is kept fixed. I searched 
> for some information about how to do it with GROMACS, but I didn't find 
> anything. 
> Could anybody give me some suggestions about this subject, please?

You could create a custom posre.itp (using genrestr) to restrain whatever atoms 
you choose, but it won't speed up your calculations in any way, if that's what 
you're after.  You could also specify freezegrps in the .mdp file, which 
requires a custom index group; it may be more difficult to use this setup based 
on the types of exclusions that would be necessary within whatever is frozen.


> Many thanks in advance and regards.
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "If you think you're too small to make a change, try sleeping with a 
> mosquito"


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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