Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem seems to occur when the molecule crosses pbc, since the first sign of the simulation not working fine after ~3ns is " Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger than the 1-4 table size 2.400 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 " where 6 and 8 are connected via a bond. After that, several lincs warnings are displayed, plus water molecules not being able to be settled. It ends up crashing due to errors in the domain decomposition " -909 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group " although I'm positive this is the consequence of all I described above. This might be the relevant part of my mdp, integrator = md dt = 0.004 nsteps = 50000000 nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.4 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 vdw-type = shift rvdw-switch = 0.8 rvdw = 1.2 fourierspacing = 0.14 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d Tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 300.00 Pcoupl = Berendsen Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 6 lincs-iter = 2 lincs-warnangle = 30 I've tried, perhaps naively, using both options for periodic_molecule with the same results. I guess it's hard to tell what did go wrong, but perhaps somebody has an idea.. I thought of submitting a bugzilla, but maybe there are some more tests I could do to pin point the problem before. Any ideas? All the best, Guillem Dr. Guillem Portella MMB - Institute for Research in Biomedicine Parc Cientific de Barcelona http://mmb.pcb.ub.es/~gportella _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
