[gmx-users] Center of mass motion removal for partial filled PBC box
wuyb02 at gmail.com
Thu Jan 27 18:25:29 CET 2011
I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P.
*J. Phys. Chem. B* *2003*, *107*, 1345-1352.
The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer
carbon sheet. After equilibration, the water droplet is around 3.5nm in
radius. A large part of the box is vacuum. Periodic boundary condition (PBC)
is applied. Graphite is fixed throughout the simulation.
>From the manual, the "comm_mode=Linear" option should be applied, which
means the translational motion of the center of mass of the water droplet
should be removed. My first question is: If the time step is 2fs, what's the
recommended value for nstcomm? (nstlist is updated very 3 time step)
Also in the manual and this mail list, it's mentioned that for non-PBC,
isolated system, "comm_mode=Angular" should be applied. Does this also
applied to my partial filled PBC box?
Do let me know if the question is not clear.
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