[gmx-users] Too many LINCS warning

[Justin Lemkul]

On 10/19/15 6:33 AM, Anahita Khammari wrote:
> Dear gromacs users,
> I am doing md simulation of protein-ligand complex, using gromacs 5.0.4.
> I did energy minimization and nvt and npt equilibration steps, without any problems.(I checked trajectory files related to the above steps and controling parameterssuch as potential energy, T, P and Density).
> Now, in md step (5000000 step), after about 300000 steps, mdrun stoped. In this case,I encountered with following error in md.log file:
> Fatal error:Too many LINCS warnings (1000)If you know what you are doing you can adjust the lincs warning threshold in your mdp fileor set the environment variable GMX_MAXCONSTRWARN to -1,but normally it is better to fix the problem
> What is the resaon of this issue? How to resolve this problem?

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

> Where and how to set the environment variable GMX_MAXCONSTRWARN to -1?

An environment variable is set in your shell.  But this is not a valid solution.

> When I repeated gmx mdrun, three times. Each time, the number of LINCS warning was changed. Why?

Welcome to the randomness associated with running MD simulations :)

-Justin

> In addition, some pdb files, related to some frames, were created.
> Please find one of these pdb files in the following link:
> https://www.dropbox.com/s/sga2u2hvfkig03x/step502017b_n7.pdb?dl=0
> Unfortunately, structure of my system in these pdb files is unusual and different from thatof files related to nvt or npt steps.
> What is the resaon of this issue? How to resolve this problem?
> Any help will highly appreciated. ------------------------------------------------
> Anahita KhammariPhD student of BiophysicsTarbiat Modares UniversityDepartment of BiophysicsTehran, IRAN
> anahita.khammari at modares.ac.ira.khammari@ut.ac.ir
>

-- 
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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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