[gmx-users] Center of mass motion removal

[Alex]

Dallas,
Of course that is doable, but removing those flying molecules is not the
actual solution specially if one is interested in calculating of some
properties in presence of all molecules, rather than visualizing them. And
also, some other molecules might leave the droplet in some stages, so, by
removing those as well, nothing would remain.

Regards,
Alex

On Thu, Dec 12, 2019 at 6:09 PM 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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>