[gmx-users] first residue in chains warning issue

Ming Tang m21.tang at qut.edu.au
Sat May 23 12:39:30 CEST 2015

Thanks, Justin

For a stable system, is it true that it can be equilibrated endlessly without error?   I got LINCS errors when my protein had been equilibrated for about 50ns. Does this mean that there is some wrong with my system?

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Saturday, 23 May 2015 6:24 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue

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 conditions.



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 http://mackerell.umaryland.edu/~jalemkul

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