[gmx-users] LINCS error in MD simulation

[Sarath Chandra]

You should re-run your simulation writing out the xtc file more frequently
to check which part of the protein/ligand is having structural issues
(considering that your mdp and other settings are accurate). Also run a
g_energy to check if the energy terms are doing fine. LINCS is pointing out
that something bad is going around the neighborhood of atoms 2835 and 2836.
Check the trajectory file in vmd/pymol to confirm that nothing is wrong
with the structures.

As pointed out in this link
http://www.gromacs.org/Documentation/Terminology/Blowing_Up systemic checks
of the system, forcefield parameters, and the mdp settings will present you
with the solution of this problem.

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 11 April 2016 at 11:31, f vazifeshenas <fahim.vazifeshenas at gmail.com>
wrote:

> Thanks a lot for your guidance.
> I was trying to Run this protein with ligand for 20ns and in first 11ns of
> it i did get this LINCS error.
>
>
>
> 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
> -------------------------------------------------------
>
>
> I have read the link and it referred to system blowing up.
> How can i be assured  that my system is blown up? and if it is it right to
> use "-append" in this condition?
>
>
>
> On Sun, Apr 10, 2016 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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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