[gmx-users] Distance restraint energy terms

nikhil damle pdnikhil at yahoo.co.in
Mon Feb 8 05:44:10 CET 2010

I have already included the [distance_restraints] section in .top file. In principle fac coloumn should be multiplied with the default force constant (1000 Kj Mol-1 nm-2) and that should get reflected in the mdout.mdp file. But this does not happen. mdout.mdp file still depicts the force constant to be 1000 even though fac coloumn > 1. I wish to restrain the distance between on two atoms.

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sat, 6 February, 2010 6:10:12 PM
Subject: Re: [gmx-users] Distance restraint energy terms

nikhil damle wrote:
> Hi,
> I have applied distance restraints on my system during MD simulation through following options:
> "disre = simple" and disre_fc = 2000 in .mdp file.
> Now i wish to see the energy term corresponding to these restraints in principle to be written in .edr file. But g_energy programme does not list any term corresponding to these restraints.

Then you haven't applied any distance restraints.

> I have following 2 questions:
> 1. How one should ensure that the restraints are applied correctly ?
> 2. How should I check the corresponding energy ?

Setting distance restraints isn't as simple as setting some .mdp options, you have to have a [distance_restraints] section in the topology that describes exactly what those restraints are.  This is all in the manual, and has been discussed a number of times on the list, so there should also be some pointers in the archives.

If it works, you should see the corresponding energy term.


> Plz help ASAP
> Regards,
> Nikhil
> ------------------------------------------------------------------------
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-- ========================================

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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