[gmx-users] LINCS error in MD simulation

[Justin Lemkul]

On 4/10/16 2:48 AM, f vazifeshenas wrote:
> Dear all
> Hi
> I am trying to Run one protein with ligand and i am getting a note and an
> error as fallows:
>
> Step 5009957, time 10019.9 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000219, max 0.005436 (between atoms 2836 and 2835)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     2836   2835   90.0    0.1236   0.1005      0.1000
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.5
> Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c,
> line: 224
>
> Fatal error:
> Too many LINCS warnings (1000)
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Does anybody know to deal with this LINCS error?
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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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