[gmx-users] removal of COM
Mark.Abraham at anu.edu.au
Thu Mar 12 22:34:39 CET 2009
Sun Joo Lee wrote:
> Hello Users
> I am trying to measure the drift of molecules in the system.
> When I ran the simulation, the removal of center-of-mass of the whole
> system took place at every step.
> From the mailing list, I've found that removal of COM works by making
> the velocity of the COM to be zero by subtracting the velocity from
> every particle velocity.
> It would be very grateful if you can help me to make two points clear;
> 1) Would the magnitude to be subtracted from every particle velocity
> be the same (or different depending on the mass of the particle)?
The same. The COM is the mass-weighted center of geometry, so COM
velocity is already the rate of change of the displacement of the
mass-weighted center of geometry.
> 2) Could removal of COM make one type of molecule move in an opposite
> direction of the other molecules that move in one direction to keep
> maintain the COM of the system at its original position?
Sure. Consider a system with three particles moving to the left with
speed 3 and one particle moving to the left with speed 1.
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