[gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

gportel at gwdg.de gportel at gwdg.de
Mon Nov 24 18:05:51 CET 2008

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,


Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona

More information about the gromacs.org_gmx-users mailing list