[gmx-users] (no subject)

[Mark Abraham]

Hi,

Please keep the discussion on the list, so others can participate.

> i want all the system,solute and solvent ,will be inside the box.like
before using -pbc nojump.

If you want everything inside the box, then you have to have jumps, so
don't use nojump. What you can't have in a periodic diffusing system is
everything inside the box and no jumps.

Mark

On Tue, Jun 28, 2016 at 1:33 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> How would you like to visualize the event where a solvent molecule leaves
> the box and enters the far side?
>
> Mark
>
> On Tue, Jun 28, 2016 at 12:38 PM Sepideh Momeninezhad <
> sepideh.momeninezhad at gmail.com> wrote:
>
>> dear users, i have used -pbc nojump but most of the solvent molecules
>> diffused out of the box.how can i move them back in the box?
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