[gmx-users] Position restraining protein during equilibration stage

Justin Lemkul jalemkul at vt.edu
Wed Nov 5 00:03:34 CET 2014

On 11/4/14 5:37 PM, Agnivo Gosai wrote:
> Dear Users
> I have followed several GROMACS tutorials , specially the excellent Lemkul
> tutorials. I have seen that during NVT / NPT equilibration states the
> biomolecules like protein / nucleic acids are position restrained.
> The general reasoning is that random velocities during equilibration can
> distort the structure of the biomolecules.
> During production run the restraints are released. But , I came across a
> case where initially a restrained NVT equilibration is done followed by a
> short un-restrained NVT equilibration. Then they directly proceed to a
> production run with a NPT-styled mdp file.
> So , my questions are ;-
> (A) When we are doing equilibration with restrained biomolecules are we not
> equilibrating the biomolecule and instead only equilibrating the solvent ?

Well, a restraint is only a biasing potential, so the restrained molecule can 
move, but the amount that it moves is limited.  The solvent reorganizes a lot 
during equilibration, but there are interactions between the solvent and 
restrained molecule that optimize during this time.

> (B) When we remove position-restraining for the production runs are there
> no energy artificats that arise ?

There is a reason that data analysis doesn't begin at t=0.  A period of time is 
still required to allow fully unrestrained equilibration.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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