[gmx-users] Center of mass motion removal

[Alex]

Thanks Justin,

As I said, I have already used the "trjconv -pbc mol" and "trjconv -pbc
cluster -center" in order, to remove the COM motion of the droplet,
however, when I visualize it in VMD, the whole droplet still moves around!
Do I need to consider something else in trjconv to have the COM of the
droplet fixed at a single point for all frames of the trajectory?

Regards,
Alex

On Fri, Dec 6, 2019 at 8:45 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
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