[gmx-users] Polymer melt clumping

Justin Lemkul jalemkul at vt.edu
Sun Jul 12 17:06:47 CEST 2015

On 7/12/15 6:38 AM, Pallavi Banerjee wrote:
> Hello users,
> I am carrying out an NPT equilibration of a polymer melt system of 67
> chains of Polyacrylamide of degree of polymerization 20. The polymer melt
> system appears clumped. The system does not disperse throughout the box. To
> tackle this, I adopted a method of scaling down the box vector by 0.95,
> followed by an NPT run for 500 ps with a tau-p of 20. This I did for 6
> number of times, and followed it up with a long NPT run of 10 ns with a
> tau-p of 1.5. The system hasn't dispersed yet, and thus I do not get the
> right density. How do you fix aggregation issues as this?

10 ns is not very long for anything.  The other possibility (as is always the 
case when the model doesn't reflect reality) is that the force field parameters 
are inadequate.



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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