[gmx-users] Center of Mass removal in a specified direction

Sander Pronk pronk at cbr.su.se
Tue Oct 26 13:56:51 CEST 2010

One trick I am working with right now, is to have
- periodic boundary conditions only xy
- remove the COM motion of the water and the graphite separately. The COM motion is now removed only in the xy direction, so they are free to move in z.
- put the surface (your graphite) at coordinate 0
- enable a wall. For this wall you can specify an atom type which specifies its interaction with the rest of the system. Make a special wall atom type that only interacts with the graphite.

This way you have a system that's free to move its COM in z, but not in xy, and still stays stuck to a specific coordinate.


On 26 Oct 2010, at 13:26 , Bert wrote:

> Dear gmx-users,
> It is known that if system have an absolute reference, the removal of
> COM could lead to artifacts. However, for instance, when one water
> slab adsorbs on a freezed, infinite graphite surface, the COM motion
> is still free in x or y direction, and subsequently leads to net flows
> during long time simulations. I wanna know if there is a solution for
> this case. Any suggestions will be appreciated.
> Best regards,
> Bert
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