[gmx-users] Position Restraints

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 22 05:15:50 CEST 2010

#ZHAO LINA# wrote:
>  Hi,
> When I used the genrestr to get the posre.itp specially,
> I found it set all atom to be applied to.
> Is that okay? How could I figure out which ones should not be set to.
> A little naive questions, but I do do not know.

The answer depends on your needs.  When running genrestr without an index file, 
you can choose from any of the default groups.  If you provide an index file, 
any group can be chosen.

The default behavior of pdb2gmx is to generate a posre.itp file that restrains 
all heavy (non-H) atoms.  You can do the same with genrestr if you want, but 
again, the atoms you want to restrain depend on your goals.


> Thanks with regards,
> lina


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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