[gmx-users] position restraints in SMD

Justin Lemkul jalemkul at vt.edu
Mon Jul 16 12:31:00 CEST 2012

On 7/16/12 5:36 AM, Raj wrote:
> Hi all,
>   It may be naive but I would like to get some clear explanation in SMD ( COM
> pulling) reg. The question is, Before performing the COM-pulling (incase of
> protein ligand complex) do we need to position restrain the ligand using
> genrestr and then add the topology to the topol.top file. If not why should
> not we restrain the ligand. Thanks in advance

The initial equilibration can be approached in a number of ways that includes 
restraining both the protein and ligand or one or the other.  Restraints are 
only intended to avoid large structural changes due to reorganization of the 
solvent.  Thus you may choose to restrain the whole complex initially and then 
reduce or remove the restraints over the course of further equilibration.  There 
are no hard and fast rules.  Look into the literature and see what others 
recommend, and evaluate for yourself whether or not such a protocol is 
reasonable in your case.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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