[gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

To whom may have similar problem, that is how I solved it:

First of all, Gromacs by default uses center of mass removal (at least in
versions I use), but that is for 'whole system'. In my case I  have a
two-component system and I am interested in collecting density for one of
the components.
So, I used -fit obtain in trjconv to remove transnational movement of
component 2:

trjconv_mpi -fit translation -s production.tpr -f traj.xtc -o OUTPUT.xtc
chose component 2 and 2,

Then, I collect densities from produced OUTPUT.xtc.


Best regards


On Fri, Nov 13, 2015 at 1:38 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:

> Justin, thanks for comment.
> In fact I am going to analyze g_density, but I see center of mass moves. I
> have two-component system which has phase separated after a very long time.
> I can't redo the simulation.
> I could not mange that by tajconv.
> Can I take the final .gro file of current simulation and run it with COM
> removal to collect density?
>
>
> Best regards
>
>
> On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> Please some one help me how to remove center of mass motion in a
>>> trajectory
>>> which is already created without  this setting? is that possible?
>>>
>>>
>> Not using COM motion removal during the run leads to artifacts; no amount
>> of post-processing will fix that.  If you're just looking to re-center some
>> molecule(s) of interest, that's what trjconv is for.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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