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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 23 03:22:04 CEST 2011

On 23/08/2011 10:49 AM, Dr. Vitaly V. Chaban wrote:
>> 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...

It is known that PR barostat can have problems in non-equilibrium 
situations when the time constant is short enough. See manual discussion 
of PR. Doubtless more detail can be had elsewhere.


> Vitaly
>>> 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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