NaN means "not a number" and usually it means some force went to infinity and thus your system is exploding.
running on a larger cluster won't be of any help, you have to move one step back and perform a proper energy minimization. if the error persists, you should also check your topology for anything spurious leading to energy/forces to infinity. On Mon, Jun 8, 2015 at 11:41 AM, chitrala kumaraswamynaidu < [email protected]> wrote: > Dear Andre sir, > > Thank you for your reply. I have gone through the threads but I didn't got > the exact solution for my problem. > > I have run the protein-ligand system upto nvt.tpr mdrun execution steps > in my laptop with Ubuntu. It is running comfortably but showing the output > -nan. Therefore, I thought to run it on the bolden cluster in our institute > in that it is showing the following error. > > Will use 108 particle-particle and 12 PME only ranks > This is a guess, check the performance at the end of the log file > Using 120 MPI threads > Using 1 OpenMP thread per tMPI thread > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > > ------------------------------------------------------- > Program gmx, VERSION 5.0.4 > Source code file: /share/apps/src/gromacs-5.0.4/src/gromacs/mdlib/pme.c, > line: > 7 > 54 > > Fatal error: > 2 particles communicated to PME rank 4 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension x. > 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 > < > https://uscmed.sc.edu/owa/redir.aspx?C=yM9xud_v1UCcNWWL-kM_GJgAd3dac9JI8UROBD4C7QFS8Rm-Bi1ts3jy27V4QHa_v159NARSf4A.&URL=http%3a%2f%2fwww.gromacs.org%2fDocumentation%2fErrors > > > > Thank you sir once again for your valuable reply. > > > > Yours sincerely, > > *Dr. C.Kumaraswamy Naidu, Ph.D.* > Post doctoral Fellow Bioinformatics, > Department of PMI, School of Medicine, > University of South Carolina, > Columbia, South Carolina 29208 > > > On Fri, Jun 5, 2015 at 5:05 PM, André Farias de Moura <[email protected]> > wrote: > > > the error message is self-explaining and provides the web link you should > > have followed before posting here (you should also have checked the > mailing > > before posting, this is a recurring topic) > > > > On Fri, Jun 5, 2015 at 5:55 PM, chitrala kumaraswamynaidu < > > [email protected]> wrote: > > > > > I have run the following command on the Cluster server and I got the > > > following error. Can anyone Please help me why I am facing this error. > > > > > > gmx mdrun -deffnm nvt_2 -v > > > > > > Reading file nvt_2.tpr, VERSION 5.0.4 (single precision) > > > Changing nstlist from 10 to 25, rlist from 1.4 to 1.433 > > > > > > > > > Will use 108 particle-particle and 12 PME only ranks > > > This is a guess, check the performance at the end of the log file > > > Using 120 MPI threads > > > Using 1 OpenMP thread per tMPI thread > > > starting mdrun 'Protein in water' > > > 50000 steps, 100.0 ps. > > > > > > ------------------------------------------------------- > > > Program gmx, VERSION 5.0.4 > > > Source code file: > /share/apps/src/gromacs-5.0.4/src/gromacs/mdlib/pme.c, > > > line: > > > 7 > > > 54 > > > > > > Fatal error: > > > 2 particles communicated to PME rank 4 are more than 2/3 times the > > cut-off > > > out of the domain decomposition cell of their charge group in dimension > > x. > > > 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 > > > < > > > > > > https://uscmed.sc.edu/owa/redir.aspx?C=yM9xud_v1UCcNWWL-kM_GJgAd3dac9JI8UROBD4C7QFS8Rm-Bi1ts3jy27V4QHa_v159NARSf4A.&URL=http%3a%2f%2fwww.gromacs.org%2fDocumentation%2fErrors > > > > > > > > > > regards, > > > > > > Dr. Naidu > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > > > > > > > -- > > _____________ > > > > Prof. Dr. André Farias de Moura > > Department of Chemistry > > Federal University of São Carlos > > São Carlos - Brazil > > phone: +55-16-3351-8090 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
