Hi, I get the same error, but the information written in my log file is as :
Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.26180e+04 5.53024e+04 6.50084e+02 -2.83474e+02 8.50267e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06730e+05 7.84233e+04 -7.99529e+03 -9.89064e+05 -2.54063e+04 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.03982e+05 3.53794e+05 -5.50188e+05 4.26000e+02 -1.34125e+02 Pressure (bar) Constr. rmsd -1.97048e+04 5.76582e-04 The temperature is around 400, it seems normal, but the pressure is negative! Is it the problem which causes my system get this fatal error? I changed the pressure coupling to Berendsen and decrease the time step to 1fs. How would I be sure that my modifications is beneficial? By checking the pressure in log file passing the time? I would be appreciate you to help me. Thanks in advance. Sincerely, Shima ----- Forwarded Message ----- From: Shima Arasteh <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Friday, February 8, 2013 5:42 PM Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off Doesn't that mean the npt should be done for a longer time? Sincerely, Shima ________________________________ From: Mark Abraham <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Friday, February 8, 2013 5:37 PM Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi <[email protected]>wrote: > dear sir, > how can i remove this following problem > > Energies (kJ/mol) > Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 > 2.36059e+03 3.53976e+02 7.34586e+00 7.00084e+03 2.02621e+03 > LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential > 7.70414e+03 -5.91044e+04 -6.76092e+03 1.80260e+00 -4.64104e+04 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 6.48550e+04 1.84446e+04 1.84446e+04 1.88479e+03 7.32453e+03 > Constr. rmsd > 4.81184e-01 > > > ------------------------------------------------------- > Program mdrun_d, VERSION 4.5.5 > Source code file: pme.c, line: 538 > > Fatal error: > 1 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 > ------------------------------------------------------- > Did you try following the link mdrun suggested? :-) Mark -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
