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

Rafael I. Silverman y de la Vega rsilverm at ucsc.edu
Thu Sep 5 06:19:10 CEST 2013

Did you follow the link in the error message?

On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi <golshan.hejazi at yahoo.com>wrote:

> 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?
> Thanks
> 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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