[gmx-users] MD => system exploding

Chih-Ying Lin chihying2008 at gmail.com
Sun Oct 5 17:34:22 CEST 2008

When I run MD, my system is exploding.
And, I found after minimisation, the atoms of my molecule are seperated apart.

The overall charge of my system is +1,  and I put one molecule in the
gas phase to do the structure test. But, it was already exploding.

Is it hard for a +1 charge molecule to maintain a good shape under MD
What are the procedures to test and determine the mistakes I made?

Thank you

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file fullmd.tpr, VERSION 3.3.3 (single precision)
Loaded with Money

starting mdrun 'azoct'
100000 steps,    100.0 ps.

Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is
larger than the 1-4 table size 1.000 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
step 10, will finish at Sun Oct  5 06:17:20 2008
Program mdrun, VERSION 3.3.3
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 -2147483648. It should have been within [ 0 .. 5832 ]


"She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)

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