[gmx-users] Center of mass motion removal

[Alex]

Dear Justin,
As you recommended I invoked the trjconv -pbc cluster and trjconv -center
separatedly, and also, I used a proper reference .gro file (where
everything is intact) in tpr file.

Here are the command I invoked in order on my trajectory:

1. gmx trjconv -f orig.xtc -o mol.xtc -pbc mol ...
2.  gmx trjconv -f mol.xtc -o mol.clus.xtc -pbc cluster ...
3. gmx trjconv -f mol.clus.xtc -o mol.clus.center.xtc -center yes ..

After that I generated a movie out of the final trajectory, please see the
below link.

https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv

Everything is convincing and the droplet is mostly located in the center of
the box, except the times (0.03, 0.04, 0.16 seconds) when one or two of the
molecules (out of 200 molecules) leave the droplet causing sudden
considerable drifts in the whole droplet.

So, I wonder how I can fix that little issue so that the droplet stay in
center of droplet even if one or two molecules leave the droplet?

Thank you
Alex

On Sat, Dec 7, 2019 at 6:31 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/6/19 4:37 PM, Alex wrote:
> > 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!
>
> I don't know if -pbc cluster and -center simultaneously work since they
> are both applying translational changes to the coordinates. Try them
> separately.
>
> > 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?
>
> Your reference structure (in the .tpr) may need to be generated from an
> intact droplet, if that's relevant (e.g. the droplet is not formed at
> the start of the simulation and comes together over time).
>
> -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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> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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