[gmx-users] LINC warning after long time simulations

[Justin Lemkul]

On 11/30/15 5:01 PM, 凌未风 wrote:
> Hi All:
>
> I pasted this once several days ago but no one replied. I know there are a lot of questions in the forum regarding LINC warning, but my problem seems quite strange. So I write here again.
>
> My simulation system contains lipids and proteins, I am using gromos53a6 for the proteins and reaction field to deal with the long range electrostatic interactions for some reason.
> My systems keep on complaining about LINC warning, such as some angle rotated more than 30 degrees, after very long simulations (one after 140 ns simulations, the other after 450 ns simulations).
> I searched the website of gromacs regarding blowing up as well as the forum for discussions, however, my problem seemed not because of bad initial conformation or unreasonable pressure or temperature coupling.
> I suspect if the problem is due to the topologies of the lipids I was using, because the topologies of lipids were built by myself. So I also run simulations of single lipids in solution and the topology works fine.
> So I am really confused.
> I really appreciate if anyone could give me some suggestions regarding this strange problem. Is it ok to set the GMX_CONSTRWARN to -1 or I should do something else to solve this problem.
>

You should never ignore LINCS warnings. They indicate a fundamental instability 
in the system. If the simulation goes for a long time, this just indicates that 
you have a subtle problem (probably in the topology or somewhere in the .mdp 
settings) that leads to an invalid physical model.

-Justin

-- 
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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

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