[gmx-users] Incuding position restraints

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 22 19:35:37 CET 2008

DimitryASuplatov wrote:
> Hello,
> I want to impose position restraints on chains a and b with fc=1000 1000
> 1000 but to fully release some residues at the same time.
> My topology file looks like this
> ; Include chain topologies
> #include "1klc_A.itp"		- chain a topology 
> #include "posre.a.1000.itp"     - fc=1000 posres on chain a
> #include "posre.a.unc.0.itp"    - fc=0 for some chain a residues
> #include "1klc_B.itp"           - the same for chain b
> #include "posre.b.1000.itp"
> #include "posre.b.unc.0.itp"
> I include topologies considering that the next will "rewrite" the
> previous.
> Will that do?

Create index groups for the groups to which you wish to apply position 
restraints, and pass it to genrestr (in version >= 4.0) or genpr (version <= 
3.3.3).  Then only the selected residues will be involved in the position 


> Thanks.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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