zcwang wrote:
Yeah, maybe my discription is a little bit complicated.
Well, what I understand of the center of mass removal, e.g. linear
removal, is that, the center of mass is not actually contrained or
restrained, it's just that all velocities in the system are simply
substracted by the velocities of the COM of the group every nstcomm
steps.
So in fact, the COM of the group is still moving in absolute space,
right?
The COM of the system is stationary unless you have periodic boundary
condition (in which it fluctuates).
The overall velocity is subtracted from all the atomic velocities.
For example, if I add a force to a protein in a water enviroment while I
set the COM of the protein to be removed linearly, then the protein will
not actually stay stationarily in terms of COM as to the water
environment, but it will be dragged in the water environment, feeling
the friction of water mainly in the direction against the pulling
direction.
You probably wat to give the protein and the water opposite force such
that the net force is zero. Or else I don't understand what you want to
do...
I wonder if my understanding of the COM removal algorithm is right.
在 2008-10-20一的 15:52 [EMAIL PROTECTED]
zcwang wrote:
Hi all
I would like to know how gromacs remove center of mass motion?
The COM velocity is the rate of change of the position of the COM,
i.e.
the mass-weighted average velocity of the particles. If you subtract
that from each particle velocity, the COM velocity becomes zero.
Likewise for angular motion, if applicable.
I thought it still allowed center of mass motion, but just did a
transformation of the coordinates at a certain frequency.
I've never heard of GROMACS doing anything like that for this purpose.
It's just like looking at the system in a noninertial system
attached to
the COM of the group.
Is that right?
I don't know what you mean.
Mark
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