[gmx-users] Center of mass motion removal

[Albert]

I also frequently encounter this headache problem. Is it possible to 
center the protein in the pbc box during simulation? As far as I know 
Desmond has a function to do this, so that we don't need to do anything 
else to recenter our protein in the box.

Albert




On 12/13/2019 11:51 PM, Alex wrote:
> 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
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>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
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