[gmx-users] Overflow problem with test-particle insertion

Berk Hess gmx3 at hotmail.com
Thu Sep 9 09:39:42 CEST 2010


This is an interesting issue.
The chance is quite small that this happens, but maybe not negligible.
In single precision the maximum a float can store is 2^127.
This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.
The chance of inserting a particle within this radius is dens*3e-10,
where dens is the number of particles per nm^3.
A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8.
Such insertion numbers can be reached, so we probably have to worry about this.

However, in your example the distance seems to be around 4e-3, which would
give r^-12 = 6e28. This still fits in a float and should not cause problems.
So we should make sure we understand what's going on here.
Could you file a bugzilla with the files to reproduce this and which insertion
is the problematic one?

I so two possible solutions:
Force tabulated potentials with TPI, this can currently be achieved by setting
the environment variable GMX_FORCE_TABLES
Or require double precision.
But I think both solutions would lead to about 40% lower performance.


Date: Wed, 8 Sep 2010 21:16:46 -0400
From: kdaly at princeton.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] Overflow problem with test-particle insertion

Hello Gromacs users,

I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. 

I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and it seems the problem is still there. Does anyone know how to work around or fix this problem without using tabulated potentials?


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