[gmx-users] particle decomposition with distance restraints

Da-Wei Li lidawei at gmail.com
Thu Dec 13 16:40:27 CET 2012

Dear Gromacs users

I recently tried distance restraints simulation and  I have been forced to
use -PD (particle decomposition) because domain decomposition doesn't work
with distance restraints. However, my MD run will crash randomly for some
of my proteins but works well for others. Once it is crashes, I try to
rescue it by restart it using CPT file. Some times, the simulation can pass
the crash point and continue for a long time and some times it just keep
crashing. The only work-around I found is to turn off lincs. Does this mean
a bug in the code? I observed this for 4.5 and 4.6.



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