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

Golshan Hejazi golshan.hejazi at yahoo.com
Fri Sep 6 18:48:26 CEST 2013

Dear Rafael,

Thanks for your reply.
Yes, I did follow the link. This means that the system is not equilibrated well. I tried to perform some more minimization but it seems that steepest decent have already minimized it well. 
Therefore I decided to perform MD at lower T. I tried 5ns of NVT simulation at 20K and another 5ns at 50K. But still as soon as I turn on the barostate ... the simulation crashes.

Do you have any other suggestion?

 From: Rafael I. Silverman y de la Vega <rsilverm at ucsc.edu>
To: Golshan Hejazi <golshan.hejazi at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, September 5, 2013 12:19 AM
Subject: Re: [gmx-users] simulation explode while switching from NVT to NPT

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?
>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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