[gmx-users] LINCS WARNING

[Justin Lemkul]

On 10/6/15 3:26 AM, Vy Phan wrote:
> Dear all gromacs Users!
> I want to run a simulation with the system protein-ligand (I have several
> ligands).
> With EM, nvt, npt step I put position restraint for the ligands and all
> thing was fine. After that, I run production simulation without position
> restraint of ligands. I saw the ligand move out of the initial position and
> simulation was stopped.
>
> Did the LINCS warning  happen because this system is not stable ?

Yes.

> How can I keep the continuous running simulation without the  LINCS
> warnings? I want  the ligands are free to move and find their binding sites.
>

Either your ligand topology is not stable or your run settings are not sensible. 
  Please see any of the million or so posts in the gmx-users mailing list 
archive regarding similar or identical situations.

-Justin

> This is the warnings:
> 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
>
> Thank you so much for any suggestions
> Tuong Vy
>

-- 
==================================================

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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