[gmx-users] neighborsearching in semiisotropic systems

[Justin A. Lemkul]

How about equilibration?  Your first message mentioned that you might suspect a
water molecule is to blame.  Did you restrain the peptide and perform any sort
of NVT or NPT ensemble to equilibrate your solvent?  It might also be useful to
see your full .mdp file in case we might be able to spot any errors.

-Justin

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

> Dear Justin,
> the system is well minimized. I performed a steepest descent
> minimization followed by a conjugate gradient minimization and then
> minimize it again with steepest descent. The problem occurred after 3ns
> or in the second run after 5ns so I do not think it is a problem of
> minimization .
> Till
>
> Justin A. Lemkul schrieb:
> > 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/
> >
> > ========================================
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>
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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/

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