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? Thanks G. ________________________________ From: Rafael I. Silverman y de la Vega <rsilv...@ucsc.edu> To: Golshan Hejazi <golshan.hej...@yahoo.com>; Discussion list for GROMACS users <gmx-users@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.hej...@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 >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
