[gmx-users] LINCS error in MD simulation

[Mark Abraham]

Hi,

It seems likely that you've changed something before this restart, which
may not have been a good idea. What did you actually do?

Mark

On Mon, 11 Apr 2016 08:11 Sarath Chandra <sarathchandradantu at gmail.com>
wrote:

> 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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