[gmx-users] Position Restraints MD

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 12:48:15 CEST 2019

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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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