[gmx-users] nsgrid error

[Yang Ye]

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 (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...
>   
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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>>     
>
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