[gmx-users] nsgrid error

[Attilio Vargiu]

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 (gmx-users at gromacs.org)
---------

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.

Thanks in advance,
ciao
Attilio


-- 
Attilio Vittorio Vargiu
PhD Student in Statistical and Biological Physics
SISSA/ISAS, via Beirut 2-4, 34100 Trieste, Italy
Tel. 00390403787335
Fax. 00390403787528


----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/