Hi,There can be many reasons for such problems.I assume you use solvent.One
option is that you could have made your whole proteina single charge group.
grompp in Gromacs 3.3.3 checks for this,but older versions do not.Berk.> From:
[EMAIL PROTECTED]> To: gmx-users@gromacs.org> Date: Thu, 8 May 2008 14:54:27
+0200> Subject: [gmx-users] crash nsgrid.c> > > Dear all,> During my
simulations of a GFP protein (force field made with amber, > then converted to
gromacs), I usually get this error:> > Fatal error: ci = 8108 should be in 0 ..
7937 [FILE nsgrid.c, LINE 218]> > What this that means?> > If I restart the
simulation from the frame just before the crash, the > run is ok for a
(random) time and then it crashes again.> I checked this on different kind of
machines and I get always the same > behavior.> > To make things clearier, I
include the input.mdp file:> > title => cpp
= /lib/cpp> include => define =>
integrator = md> dt = 0.002> nsteps
= 500000> nstxout = 10000> nstvout
= 0> nstlog = 500> nstenergy = 500> nstxtcout
= 500> energygrps = System> pbc
= xyz> nstlist = 15> epsilon_r = 1.> ns_type
= grid> coulombtype = pme> vdwtype
= Cut-off> rlist = 0.8> rcoulomb = 0.8> rvdw
= 0.8> tcoupl = Nose-Hoover> tc-grps
= System> tau_t = 2.0> ref_t
= 300.00> pcoupl = Parrinello-Rahman> pcoupltype
= isotropic> tau_p = 4.0> compressibility =
4.5e-5> ref_p = 1.0> gen_vel = no> gen_seed
= 173529> constraints = All-bonds>
constraint_algorithm = lincs> shake_tol = 0.0001> > Any
suggestion is welcome.> > Thanks> > F.A.>
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