[gmx-users] periodic boundary issue

Berk Hess gmx3 at hotmail.com
Thu Dec 11 10:12:01 CET 2008


I have not heard before about such problems.

What did you do exactly?
Did you continue your simulation the old fashioned way:
tpbconv with a trajectory file?

In 4.0 there are checkpoint files which can be read by mdrun -cpi,
so you only need tpbconv to increase the number of steps in your tpr file.

But the old fashioned way should still work.
If there would be a pbc error I would expect the problems you describe
to occur at step 0.

Are you running in parallel?


Date: Wed, 10 Dec 2008 19:32:18 -0800
From: pwhitfor at ctbp.ucsd.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] periodic boundary issue

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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