Hi Magnus,
Thanks for the response.
As I said before the system contains the "thin film + molecule A ( single
molecule) intended for the PMF calculation + Water".
And actually by the “comm-grps = thin film” the gmx grompp failed as some
atoms are not part of any center of mass motion removal group (VCM groups).
However, the two following options work:
“comm-grps = thin_film Mol_A SOL”
or
“comm-grps = Other SOL”
Where the Other group contains the thin film and molecule A, the
pull_group2 and pull_group1, respectively.
Which one do you recommend, please?
Thank you
Alex
On Mon, Mar 23, 2020 at 08:57 Magnus Lundborg <magnus.lundb...@scilifelab.se>
wrote:
> 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
>
>
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