[gmx-users] Re: parallel job crash for large system

Dr. Vitaly V. Chaban vvchaban at gmail.com
Tue Aug 23 02:49:46 CEST 2011

> On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote:
>> In the below issue, the barostat is setup semiisotropically and works
>> only along the "long" direction. The density of the system slowly
>> grows due to mixing. If this can be useful....
> Does a different barostat work?

No idea. Should try. Do you think it is a barostat issue? There were
two systems on the first stage, ~6x6x8nm and ~6x6x22nm. They were OK,
also with semiisotropic pressure coupling. Then the boxes were merged,
so that the interface of two liquids forms. Again, after several
hundreds of ps (not fs!) of this interface simulation there are no
problems and then suddenly error occurs. Of course, I am pretty sure
about the force fields, starting configuration, etc, etc...


>> On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban
>> <vvchaban at gmail.com>  wrote:
>>> We are running the system consisting of 84000 atoms in
>>> parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and
>>> evolution of trajectory is reasonable but after several hundred
>>> thousands of steps it suddenly crashes. Mysteriously, each time it
>>> crashes at different time-steps, but it always occurs. The parts of
>>> this system were equilibrated separately and did not crash. The system
>>> is not in equilibrium but without external forces. The
>>> Parrinello-Rahman barostat is turned on. The md.log does not show any
>>> problems, the PDB configurations are not written down before crash,
>>> the constaints are absent, the time-step is 1fs that is OK for
>>> separate components (in separate boxes).
>>> With serial gromacs, the error is not yet observed, but given the size
>>> the run is very slow.
>>> What can it be? Can it be somehow connected with the very (oblongated) box?

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