[gmx-users] Cutting simulatio box

[Tsjerk Wassenaar]

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.