[gmx-users] Polymer Relaxation Issue

Justin Lemkul jalemkul at vt.edu
Mon Jan 13 23:51:35 CET 2014

On 1/13/14, 5:21 PM, decaiyu wrote:
> Dear All,
> I created a polymer topology with Gromos43a1.ff force field.
> I am running simulation to try to validate my force field.
> When I run a NVT (300K) simulation for 500 ps for a 50-unit polymer without
> periodic boundary conditions, it seems that the polymer just vibrates
> without signifcant relaxation from its initial configuration.
> But when I do the same NVT simulation for the same polymer structure with
> COMPASS force field with Materials Studio, the polymer quickly relaxes (from
> a linear polymer into a coiled structure).
> What could be the issue here? The dihedral potential and the bond angle
> potential too strong, or the vDW potential attraction is not strong enough?

It sounds like you have some sort of restraints applied during the simulation, 
but without a complete .mdp file, there's no way to tell.



Justin A. Lemkul, Ph.D.
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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