[gmx-users] Re: How do gromacs remove center of mass of a group?

[zcwang]

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
A )fixed.

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

thanks


Below is the 4 previos mails in this topic, for convienence. I just
don't know how to reply the mailing-list digest properly.

======================================================

 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 +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,
>> 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
> 
> ________________________________________