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

Faezeh Pousaneh fpoosaneh at gmail.com
Fri Nov 13 13:39:40 CET 2015


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
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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