[gmx-users] Re: How do gromacs remove center of mass of a group?
zcwang at mdl.ipc.pku.edu.cn
Tue Oct 21 13:44:15 CEST 2008
Oh, in fact I've posted a relevant topic earlier, but receive no reply.
Here I want to do an AFM simulation using gromacs, pulling at the COM of
a protein A, while keeping the COM of another protein B (which binds to
I do use pbc condition, and SPC water solvent sorrounding.
I know I need simply add a restraint spring potential on the COM of B,
but don't know how to implement it in detail.
I notice that gromacs has a COM motion removal option and I might be
able to remove the COM motion of B. But I think it does not actually do
what I wanted, because I understand COM motion removal as simply
substracting the velocity of whole system by the COM of B every nstcomm
steps, it's like a transformation of coordinates which always set the
COM of B as the origin, while the motion of the system actually remain
the same as to no COM motion removal.
So briefly, I just want to make sure 2 things:
1. how to fix the COM of a group
2. the algorithm in gromacs used to remove the COM motion
Below is the 4 previos mails in this topic, for convienence. I just
don't know how to reply the mailing-list digest properly.
> 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
> So in fact, the COM of the group is still moving in absolute space,
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
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
> I wonder if my understanding of the COM removal algorithm is right.
> 在 2008-10-20一的 15:52 +0200，gmx-users-request at gromacs.org写道：
>> 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,
>> 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.
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