[gmx-users] neighborsearching in semiisotropic systems

[Berk Hess]

Hi,

Did you check how your box dimensions evolve?

For a homogeneous system (as your small test system)
one should not use semi or anisotropic pressure coupling,
since the box shape can distort unlimitedly causing
the system to crash.

Berk.


> Date: Tue, 3 Jun 2008 17:00:14 +0200
> From: till at bph.rub.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] neighborsearching in semiisotropic systems
> 
> 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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