[gmx-users] simulation explode while switching from NVT to NPT

Golshan Hejazi golshan.hejazi at yahoo.com
Thu Sep 5 04:17:04 CEST 2013

Hi everyone,

I am simulating a system of paracetamol crystal in ethanol solvent. I used pdb2gmx to generate the topology and gro file and I minimized the system using steepest decent. As long as I perform NVT simulations at any temperature, the simulations goes on! But as soon as I switch from NVT to NPT, the simulation crashes with the following error:

I tried to perform NVT at very low temperature, say 50K and then switch to NPT ... but no WAY!
Can you help me with that?


Warning: 1-4 interaction between 1361 and 1368 at distance 10600663849073184.000 which is larger than the 1-4 table size 1.800 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 4.5.4
Source code file: pme.c, line: 538

Fatal error:
9 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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