Dear all, running a box of neat water with the below mdp file in GROMACS 4.5.1 results in a fast linear increase of the volume of the box, the water getting torn into clusters. The same simulation in 4.0.7 (with nstcalcenergy removed, of course) runs just fine, with the box volume stable and fluctuating. In 4.5.1 the problem can be fixed by setting nstlist = 1. I assume this would also be the case for other positive numbers. The same behavior can be seen for the Parrinello-Rahman barostat. I can of course provide full testcases ready to run, if needed.
This looks like a bug to me. Can anyone help me resolve this? Thanks, Ondrej ; RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.002 nsteps = 5000 comm-mode = Linear nstcomm = 10 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstcalcenergy = 10 nstenergy = 100 nstxtcout = 100 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = -1 ns_type = grid pbc = xyz periodic_molecules = no rlist = 1.3 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME-Switch rcoulomb-switch = 0.6 rcoulomb = 0.8 vdw-type = Shift rvdw-switch = 0.6 rvdw = 0.8 DispCorr = EnerPres fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t = 0.5 ref_t = 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = none -- 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