[gmx-users] Position Restraints

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Wed Sep 22 05:19:14 CEST 2010

Thanks for your answer.

How can I tell which ones I should restrain? all no-H atoms? in most general situations.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints

#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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