[gmx-users] On the ussing of different equilibration protocols in NPT

Justin Lemkul jalemkul at vt.edu
Sat Sep 27 22:44:39 CEST 2014

On 9/27/14 3:05 PM, James Starlight wrote:
> Dear Gromac's users!
> According to tutorials I've noticed that It's important to use position
> restrains on the protein (and lipid in case of membrane) during npt
> equilibration phase. But in my mind the presence of the restrains on some
> part of the system during introducing to some preassure bath (Which act
> like piston) should produce alot of errors on the stability of the whole
> system shouldn't it? Does alternatively Parrinello barostat using in
> Gromacs has completely different preassure coupling method in comparison to
> langevins piston (in namd)

If the reference coordinates are not similarly scaled, then yes, you can get 
artifacts.  But in general, any pressure-related artifacts from restraints would 
pale in comparison to simply starting an unrestrained equilibration in a 
pseudo-crystalline environment built by stacking water boxes around the solute.

Restraints on membranes are rather uncommon and are used mostly in cases of very 
badly behaved systems.  Equilibrating membranes requires a lot of unrestrained 
time.  This is the same reason why the initial frames of a simple 
protein-in-water system are also eliminated.  Despite equilibration, the system 
is still generally not at equilibrium for some time.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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