[gmx-users] Cutting simulatio box

[Faezeh Pousaneh]

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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