[gmx-users] Distance restraint energy terms

[Mark Abraham]

On 08/02/10 16:18, nikhil damle wrote:
> 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 ?

You'll stand a better chance of a useful answer if you quote your usage 
of such indices in your .itp file. Manual 4.3.4 has an example.

Mark

> Regards,
> Nikhil
>
> ------------------------------------------------------------------------
> *From:* nikhil damle <pdnikhil at yahoo.co.in>
> *To:* jalemkul at vt.edu; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *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 <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.
>
> -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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