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.
Mark
Vitaly
On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban
<vvcha...@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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