[gmx-users] Center of mass motion removal

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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