[gmx-users] re: simulation-rigid

Justin A. Lemkul jalemkul at vt.edu
Tue May 10 23:02:20 CEST 2011

Frank Neuhaus wrote:
> Hi,
> I have a protein simulation in which all residues simulate correctly 
> with the exception of five in a loop.   These five out of 360 are in a 
> loop (or bend) separate from my area of interest.  Thus, I would like to 
> treat them as a rigid sequence.  Using the position restraints in the 
> posre.itp file does not help me.  I am looking for a script that I can 
> write into my mdp files that restricts all simulation in these five 
> residues.   Can anyone help me with this little issue?  Thank you.

You can use freezegrps to completely prevent any changes to the coordinates. 
Whether or not this makes any physical sense or will have any artifactual 
influence on the rest of your protein is up to you to decide.  Note that (if I 
recall correctly), you cannot use an NPT ensemble when applying freezegrps due 
to the coordinate scaling intrinsic to the barostat algorithms.



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


More information about the gromacs.org_gmx-users mailing list