[gmx-users] Center of mass motion removal for partial filled PBC box

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 28 01:07:20 CET 2011

On 28/01/2011 4:25 AM, WU Yanbin wrote:
> Dear GMXers,
> 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.

I'm not sure what PBC is gaining for you. I think you want vacuum 
boundary conditions, which may as well be non-periodic.

> 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)

10 is probably fine.

> 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?

No, this is referring to simulations like a protein in vacuum.


> Do let me know if the question is not clear.
> Thank you.
> Best,
> Yanbin

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