[gmx-users] Center of mass motion removal

[Justin Lemkul]

On 12/5/19 3:47 PM, Alex wrote:
> Hi all,
>
> I have a droplet containing two molecules types of A and B in water.
> Unfortunately, I forgot to use the comm-grps = AB flag in my mdp file of
> simulations so, the whole droplet just drifting around inside water. Now at
> this point, I wonder if there is a tool in gromacs to remove the center of
> mass motion of the whole trajectory?
>
> I have already applied the
> gmx trjconv -pbc mol
> Then
> gmx trjconv -pbc cluster -center yes
>
> However, as I knew, they can not stop the COM motion.

These are two different things. The removal of net COM motion during MD 
is to correct for artifacts associated with the accumulation of kinetic 
energy in translational degrees of freedom. In your case, however, you 
should *not* be trying to remove COM motion from solute groups. If 
everything is just in solution and you don't have any kind of 
biphasic/interfacial system, your comm-grps should simply be set to 
System. Separate groups are only needed for systems with different 
phases that may have different diffusion behavior. If you have molecules 
solvated in water, separately removing COM motion is actually artificial 
and should not be done.

Removing net motion of a given group for visualization purposes can be 
accomplished with trjconv, but this is not the same as correcting the 
trajectory for the above phenomenon.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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