[gmx-users] LINC warning after long time simulations

Smith, Micholas D. smithmd at ornl.gov
Tue Dec 1 14:20:10 CET 2015

A few things to check when trying to figure out the origin of the LINCS error that occurs only after a long run:

1) What is your time step?
2) If you restart from a previous checkpoint does the same error occur?
3) What are your LINCS settings?
4) Do you see any unphysical behavior prior to the LINCS warning?
5) At the frame with the Warning what does the structure look like? Do you have any obvious clashes? Is it your lipids that are having the LINCS error or something else (do you have a protein in your simulation interaction with the lipids)?

Even if the crash is due to something subtle, you can typically figure out what is wrong by checking the above and carefully adjusting where necessary. Good Luck.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, December 01, 2015 7:45 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] LINC warning after long time simulations

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 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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