[gmx-users] Increase temperature to 550K
chihying2008 at gmail.com
Tue Nov 10 19:27:10 CET 2009
Here is the dt and constraints.
Any other suggestion about heating up the system and make the system stable?
dt = 0.001
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
Chih-Ying Lin wrote:
> The simulation system is merely water + one lysozyme.
> I increase temperate to 550K.
> Then, the simulation broke.
> The following message is shown.
> MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
> mpiexec: Warning: task 0 exited with status 1.
> mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
> mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
> Anything wrong with the simulation?
I think, pretty clearly, yes. Increasing to a high temperature can make the
system unstable. Are you using a suitable dt? Constraints?
> Thank you
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