[gmx-users] problem with center of mass removal, rest-group, all gmx versions

Michael Brunsteiner mbx0009 at yahoo.com
Wed Dec 10 07:45:12 CET 2008

Hi everybody,

Trying to simulate a solvated protein/ligand complex
my system keeps blowing up with lincs errors after some
un-predictible amount of simulation time (anything between
10 and 1000 ps) i tried out numerous combinations of
mdp settings/parameters and gromacs versions, and nothing
seems to help, but there is one point that's still unclear
and I wonder whether this can be the problem:
In ALL my md.log files is see the following output:

We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 163113
There are: 6508 Atoms

in the mdp-documentation it says:

    group(s) for center of mass motion removal, default is the whole system

I only now noticed that i never set comm_grps explicitly,
assuming that the default (System) is ok, the comm_mode i typically
set to Linear and nst_comm to either 100 or 1, or I leave these
commands out altogether assuming that the defaults are ok ...
system blows up in each case.
My system has much more than 6508 atoms, and none of the groups in the
ndx file contains 6508 atoms, and i double and triple checked that
there is not a sigle atom that is NOT member of some group in the
ndx file ... so what is this "rest" group??  it is apparently
made automatically by grompp or mdrun. I can imagine that constraining
the center of mass of a (possibly randomly chosen) subgroup of
atoms can cause instabilities, has anybody observed something
like this before ??
I have seen a couple of mails in this list in which people describe
similar problems, but found none with a solution/explanation.

I should add that i run gromcas on an AMD64 PC,
linux 2.6.9. I also tried a 32 bit machine, and I tried gmx 3.3.2,
3.3.3, 4.0 and 4.0.2 ... always the same problem.

any help is appreciated! (sample mdp file below)


mdp-file (please mind that this is just one example,
i tried out many modifications of practically every
single parameter that might cause the problem, tried shake
varied lincs_iter, thermostate, etc...)

cpp                      = /usr/bin/cpp
integrator               = md
nsteps                   = 500000
dt                       = 0.002
nstxtcout                = 1000
xtc_grps                 = receptor ligand
nstenergy                = 100
nst_log                  = 100
nstxout                  = 10000
nstvout                  = 10000
nstlist                  = 12
nstype                   = grid
pbc                      = xyz
nstcomm                  = 100
rlist                    = 1.2
coulombtype              = PME
rcoulomb                 = 1.2
vdwtype                  = shift
rvdw                     = 1.2
tcoupl              =  Berendsen
tc-grps             =  System
ref_t               =  300
tau_t               =  0.1
Pcoupl                   = no
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
fourier_nx               = 32
fourier_ny               = 32
fourier_nz               = 32
constraints              = all-bonds
unconstrained-start      = no
lincs_iter               = 8
energygrps               = receptor ligand solvent


More information about the gromacs.org_gmx-users mailing list