[gmx-users] Why Position Restraint on Protein in NVT?

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 19:02:12 CEST 2012

On 10/18/12 12:06 PM, Arman M. Soufiani wrote:
> Dear all friends,
> I wonder why we should impose POSRES on the protein in the system while
> running NVT?! Shall we do so even for the system containing a short
> peptide?!

Velocity generation causes atoms to move randomly, which can impart nasty forces 
on your solute.  Restraining the solute helps preserve its structural integrity.

> What if I let the peptide, SOL+ions and my system's synthetic polymer apply
> T-coupling individually?

That depends on the size of each component.




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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