[gmx-users] first residue in chains warning issue

Justin Lemkul jalemkul at vt.edu
Fri May 22 22:24:05 CEST 2015

On 5/22/15 3:39 AM, Ming Tang wrote:
> Dear Justin,
> Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints?
> If the difference is quite small, then I can choose constraining bonds to increase time step.

This is generally (read: pretty much always) what people do in biomolecular 
simulations.  The bonds are rarely (read: practically never) excited from their 
ground state, so constraints are a reasonable approximation.  This isn't 
universal, but it's definitely true in most biological systems at ambient 



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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