[gmx-users] first residue in chains warning issue

[Justin Lemkul]

On 5/23/15 6:39 AM, Ming Tang wrote:
> 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?
>

A stable run should never produce LINCS warnings.

-Justin

> -----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
>
> --
> ==================================================
>
> 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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-- 
==================================================

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

==================================================