[gmx-users] Cutting simulatio box

[Faezeh Pousaneh]

You are absolutely right.

So, my objective:
I have a phase separation of a two-component system, and my aim is to
obtain the 'chemical potential' at each phase (which I know they must be
equal, since there is equilibrium). The method I've chosen is summation of
'ideal' and 'excess' chemical potentials, which the latter is obtained
through interaction of single molecule with the rest of molecules at that
phase.





Best regards


On Mon, Jul 18, 2016 at 1:25 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Faezeh,
>
> It helps if you begin with stating your objective and context, rather than
> asking for the solution to what you think is the critical issue in what you
> think is the solution of what you think your problem is. If you ask for
> water in a slab, you get an answer for water in a slab. Apparently you want
> a specific water molecule. Then you ask for a 'phase', which usually
> involves many particles, but it appears that it's that same single
> molecule? That changes matters quite a bit, as whatever you're going to
> look at is going to be pretty noise.
>
> What is your objective?
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jul 18, 2016 at 1:10 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
> > Hi Tsjerk,
> >
> > That option seemed complicated in my case, as my previous discussion with
> > Mark (titled: g_select, only 'one' water within z>=10 and z<=10.1).
> Since I
> > need the energy between 'single' molecule at specific 'z' of the box
> > indicating the phases .
> >
> > So I think my given way is easier, but not sure if the reruns goes like
> the
> > original simulations?
> >
> >
> > Best regards
> >
> >
> > On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Faezeh,
> > >
> > > You could use gmx select to make groups for the two phases and then
> > perform
> > > a rerun with these new groups as energy_grps. That would give you the
> > > within and between group energies.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" <fpoosaneh at gmail.com>
> wrote:
> > >
> > > Hi,
> > >
> > > I have a Phase-separation in my simulation result. I need to find
> energy
> > > between molecules at each phase. Can I cut the box into small boxes,
> each
> > > having one phase, and then by extension the run (with similar setting
> as
> > > original) obtain the energies at each phase?
> > >
> > > Thank you!
> > > Best regards
> > > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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