I think I could figure out the mistake I was committing.
I intended to restrain 2 pairs of distances simultaneously. Hence the index of
both the pairs were kept 1 with lower and upper bounds different for the two
pairs. This had created error. The same indices for a pair of distances would
imply they contribute to same NOE signal. Hence their lower and upper bounds
should be same. I thought the same index would only mean that the restraints on
both pairs would be treated simultaneously as written in manual and there is no
need that lower and upper bounds of the restraints should be equal for both
pairs.
Am I understanding correctly ?
Regards,
Nikhil
________________________________
From: nikhil damle <[email protected]>
To: [email protected]; Discussion list for GROMACS users <[email protected]>
Sent: Mon, 8 February, 2010 10:14:10 AM
Subject: Re: [gmx-users] Distance restraint energy terms
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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