[gmx-users] Position Restraints MD

[ISHRAT JAHAN]

Thanks Justin Sir for the response.

On Mon, Sep 23, 2019 at 4:18 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/20/19 2:10 AM, ISHRAT JAHAN wrote:
> >   Dear all,
> > I am doing MD simulation of protein and metal atom. I had applied
> position
> > restraints on metal atom. I had applied it as follows- ( kindly correct
> me
> > if i am wrong)
> > first made an index of metal atom and generated the posre_ion.itp file
> > using gmx genrestr and then added the force and atom index into the top
> > file of protein in [position restraint] part. In full.mdp file , added
> the
> > line define= -DPOSRES.
> > Then performed full md. But when i calculated the rmsd of backbone its
> > value is found to be around 0.02 nm(very small). I do not know whether
> > restraints have been applied on metal or on the whole system.  Am I doing
> > it correct or not?
>
> Using -DPOSRES is the default keyword for enabling position restraints
> on the entire protein. Given your tiny RMSD, that should confirm it.
> Visualize your trajectory and you should see that the protein isn't moving.
>
> Applying an absolute restraint to a metal ion is a curious approach.
> What may end up happening is your protein will diffuse but the metal
> will stay behind. If you're trying to enforce some type of coordination,
> use distance restraints instead.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh