[gmx-users] Center of mass motion removal

[Dallas Warren]

You could do that (maintain the "center" of the droplet in the frame) is to
remove those molecules that exit and return to the droplet, and then use
the remaining molecules as the index group to determine the COM to which
things are then centered on.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 13 Dec 2019 at 10:09, Alex <alexanderwien2k at gmail.com> wrote:

> 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
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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