AW: Simulation crash during NPT equilibration

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Apr 11 2014 - 06:31:49 CDT

If you are using fixed atoms, you might want to increase langevinpistondecay
and langevinpistonperiod to allow longer relaxation after cell size change
for high repulsion forces due coordinate rescaling. Otherwise, if your
solvent density is very low from the start (large vacuum bubbles), try
setting "margin" to a value around 4 so that the parallel patch grid can
hold the large initial cell shrinking. Otherwise, restart from the latest
restart of the NPT run, as the shrinking won't be that huge again, usually.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von James Starlight
Gesendet: Freitag, 11. April 2014 12:58
An: Namd Mailing List
Betreff: namd-l: Simulation crash during NPT equilibration

 

Dear Namd users,

I've forced with the problem during equilibration of my water-soluble
proteins during npt (adding barrostat) stage. This simulation have
accompanied with the changing of the XYZ directions of the simulation box
with the increase in Z and decrease in XY planes.

Eventually I've obtained

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
Segmentation fault
------------- Processor 1 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original patch
grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

What are the possible solution if I'd like to enable such alteration during
equilibration (useFlexibleCell= on) ?

James

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