[gmx-users] nsgrid error

[Attilio Vargiu]

> 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 (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.
>
> 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...

many thanks,
bye
Attilio


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


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