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 <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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.
-Justin
> Plz help ASAP
>
> Regards,
> Nikhil
>
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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