[gmx-users] regarding range checking error and constraint errors in Lincs algorithm

[Justin A. Lemkul]

> Program mdrun, VERSION 3.3.1
>
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
>
> Explanation: During neighborsearching, we assign each particle to a
> grid based on its coordinates. If your system contains collisions or
> parameter
>
> errors that give particles very high velocities you might end up with
> some coordinates being +-Infinity or NaN (not-a-number). Obviously, we
> cannot put these on a grid, so this is usually where we detect those
> errors.
>
> Make sure your system is properly energy-minimized and that the
> potential energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 3375 ]
>
> Please report this to the mailing list (gmx-users at gromacs.org)
>
> -------------------------------------------------------

I have seen this error when I have somehow generated bad contacts in my starting
structure, causing atoms to explode of into space.  Did mdrun generate any
step*.pdb files?  Those might give you some indication as to where the problem
lies.

>
-----------------------------------------------------------------------------------------------------------------------------------------
> t= 0.02ps Water molecule starting at atom 71500 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> previous and current coordinates
>
-------------------------------------------------------------------------------------------------------------------------------------------
> I have triend reducing the time step and I still get the same error.
> I have also pasted the pr.mdp file I use to set up and run position
> restrained dynamics.

Have you tried looking at the water molecule that contains atom 71500 to see
what it might be bumping into?  Again I suspect bad contacts.

-Justin

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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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