[gmx-users] periodic boundary issue

Paul Whitford pwhitfor at ctbp.ucsd.edu
Thu Dec 11 04:32:18 CET 2008

I am having the following issue with Gromacs 4.0.2:

I run a simulation with pbc=xyz.   By the end of the simulation my molecule
is split by the boundary (half of the molecule appears on one side and the
other half on the opposite side).  This is not a problem.  The problem
occurs when I use tpbconv to extend my run.  Then, within the first few
steps (<100 steps) of the extended run I get messages like

Warning: 1-4 interaction between 1251 and 962 at distance 69.927 which is
larger than the 1-4 table size 51.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Program mdrun, VERSION 4.0
Source code file: nsgrid.c, line: 357

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 .. 1331 ]


What appears to be happening is that when the run is extended, the pbc is
not imposed correctly, and the system explodes from all of the covalent
bonds being stretched across the length of the box.  This also occurs if I
take the final gro structure from the previous run and use grompp instead of
tpbconv.  This occured in 20 different trajectories, all of which had run
successfully with no issues for millions of time steps immediately before.

Any ideas what is going on?  I did not have this issue with the cvs version,
but once 4.0 was released I started having this trouble.

Thanks in advance

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