On 9/7/2007 2:38 PM, Attilio Vargiu wrote:
Attilio Vargiu wrote:
Hi All,
I'm simulating a drug-DNA complex in water, with the AMBER force field
and
running GROMACS in parallel on 8 processors.
After ~100 ps, I get the error here below:
---------
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or
parameter
errors that give particles very high velocities you might end up with
some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the
potential
energy seems reasonable before trying again.
Variable ci has value 3035. It should have been within [ 0 .. 2940 ]
Please report this to the mailing list ([email protected])
---------
It is not the first time I got this error, but I'm pretty sure the
system
is well equilibrated (I taken the starting structure from a previous 3ns
long simulation, I do not see anything strange visualizing the traj, and
the solute RMSD with respect to the initial configuration stays below
1.5
angs), and the potential energy is reasonable and with no drift.
Sometimes I tried simply to restart the simulation from the previous
"stable" point with coordinates, velocities and energy information
(through tpbconv), and this had fixed the problem.
Is not this a little bit strange? Could be a problem of the compiler?
I'm using the fortran compiler intel9.0, the gnu c compiler, mkl-7.2 and
mpich.
Yeah that does sound weird. My first suspect would be MPICH - try LAM.
In fact, following the suggestion by Yang Ye I tried to use a time step of
1.5 fs instead of 2, but unfortunately the run stopped just some ps
later... :-(.
Now I am trying using 1fs, but the same simulation with 4 instead of 8
processors seems didn't crash after 200 ps.
Furthermore, simply restarting the simulation with 8 procs from the last
point overcame the problem.
I think I'll try to install the LAM...
This may likely also be due to p-coupling. Switch from NPT to NVT as
long as the box sizes has been stabilized.
many thanks,
bye
Attilio
Mark
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