[gmx-users] Strange jumps in box dimensions

Igor Ariz iarizex at gwdg.de
Mon Mar 12 15:27:16 CET 2018

Hi all,

I am simulating a small membrane protein system:

Protein  1 (256 aminoacids)
DPPC    104
SOL    4377
CL    7
NA    1

using CHARMM36m force-field, short cut-offs (0.9 nm) and semi-isotropic 
Berendsen p-coupling.

I am experiencing sudden jumps in box dimensions from [6.52 6.52 6.96] 
to [5.05 5.05 7.72]
in tens of nanoseconds, which take hundreds of nanoseconds to go back to 
the previous box size.

Has anyone ever seen anything similar?


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