[gmx-users] comm-grps

[Magnus Lundborg]

Hi Alex,

Using

"comm-grps = thin film"

should be right, yes. In theory

"comm-mode = Linear-acceleration-correction"

could improve things, but is mainly useful if you are actively pulling 
the molecule through, i.e., what you are probably doing when generating 
the windows.

There was a user report the other day ("2020.1: comm broken with -update 
gpu -bonded gpu ?​") that said that comm removal did not work when 
combining update and bonded on gpu. That could be the problem in this 
case as well, especially if it turns out that it's running the bonded 
interactions on gpu that's the issue.

Cheers,

Magnus


On 2020-03-21 09:38, Alex wrote:
> Hi all,
> Using umbrella sampling and WHAM I am calculating the PMF of a single
> molecule (A) diffusion from water into a thin film made out of another
> molecule. The thin film is supposed to be an infinite film along X-Y (or
> have periodicity laterally),  also the pbc for the whole system is ON for
> all three directions pbc = xyz.
> The reaction coordinate is the film_com to A_com along Z axis.
>
> By default  the "comm-mode = Linear" for the whole system, however the thin
> film translate during the PMF simulation in each window causing some
> artifact in the resulted PMF.
>
> Now, for such system my question is that if I am allowed to use:
> "comm-grps = thin film"
> and also
> "comm-mode = Linear-acceleration-correction" ?
>
> Thank you
> Alex