[gmx-users] Center of mass motion removal

[Alessandra Villa]

Hi,

Maybe trjconv workflow below can help you to visualize your droplet
(without no com motion)

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=trjconv

Best regards
Alessandra


On Thu, Dec 5, 2019 at 9:49 PM Alex <alexanderwien2k at gmail.com> wrote:

> Hi all,
>
> I have a droplet containing two molecules types of A and B in water.
> Unfortunately, I forgot to use the comm-grps = AB flag in my mdp file of
> simulations so, the whole droplet just drifting around inside water. Now at
> this point, I wonder if there is a tool in gromacs to remove the center of
> mass motion of the whole trajectory?
>
> I have already applied the
> gmx trjconv -pbc mol
> Then
> gmx trjconv -pbc cluster -center yes
>
> However, as I knew, they can not stop the COM motion.
>
> Thank you
> Alex
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