[gmx-users] neighborsearching in semiisotropic systems

[Justin A. Lemkul]

Did you do any sort of minimization or equilibration on your system?  Usually
these errors arise because of a poor starting structure, or one that has been
insufficiently equilibrated.

-Justin

Quoting Till Rudack <till at bph.rub.de>:

> Dear users,
>
> During protein simulations occurred the range checking error of the
> neighborsearching. I checked the comments on this mistake in the user
> list and then checked my system on any hints of an exploding system but
> it seems to be stable. In order to be sure I cut down the system to a
> small peptide consisting of only ten aminoacids and used the ffG43a1
> forcefield.
>
>
> I performed 10ns simulations of this small system in a cubic
> spc-waterbox with different pressure parameters and tried single and
> double precision. I got the following results:
>
>
> For
>
> pcoupltype = semiisotropic
>
> tau_p = 0.5 0.5
>
> compressibility = 4.5E-5 4.5E-5
>
> ref_p = 1 1
>
>
> with double precision occurred the mistake:
>
>
> -------------------------------------------------------
>
> Program mdrun_d.mpi, 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 284. It should have been within [ 0 .. 200 ]
>
> Please report this to the mailing list (gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>)
>
>
> Then, I changed tau_p to 5.0 and the mistake did not occurce anymore
> during the 10 ns. With single precision the mistake never occurres. I
> also tested double precision with pcoupltype = isotropic and this also
> works.
>
> Next, I wanted to reproduce the mistake so I took the same tpr file of
> the crashed simulation with tau_p = 0.5 and started the simulation
> again. The mistake occurred again but not at the same timestep. The
> first run crashed after step 1558630 and the second run after step
> 2597500 and also the ci variable is not exactly the same (Variable ci
> has value 283. It should have been within [ 0 .. 200 ]).
>
>
> I think there might be a problem between the neighborsearching and the
> semiisotropic pressurcoupling together with double precision. I am quite
> sure that the peptide is not the problem. Maybe there is a problem with
> a water molecule. I would be glad if someone can give me an explanation
> why this mistake is not reproducable at the same timestep and why it
> occures with tau_p=0.5 and not with tau_p=5.0.
>
>
> Thanks
>
>
> Till
>
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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/

========================================