The pressure convergence seems normal. I can not understand the reason of this fatal error. I guess everything sounds normal, so what's the problem? Is it observable in my log file? Also potential , total energy are finite!
Thanks Justin. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Sunday, February 10, 2013 11:48 PM Subject: Re: Fw: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off On 2/10/13 3:14 PM, Shima Arasteh wrote: > 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? An instantaneous value of pressure is meaningless. http://www.gromacs.org/Documentation/Terminology/Pressure > 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? > Well, for one, the system won't blow up ;) The assessment of any equilibration is basically the same - do the observables of interest (temperature, pressure, etc) converge to the desired value? -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
