On Tue, Jan 25, 2022 at 1:19 PM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Jan 25, 2022, Daniel Konstantinovsky wrote:
> >
> >I want to simulate the vacuum-water interface. While invoking solvatebox
> in
> >tleap, I need to make it so that neutralizing ions are added only to the
> >bottom half of the box because I will be removing the top half of the
> >water. Is that possible in tleap? If not, what do you recommend I do,
> short
> >of manually moving the ions into the water after the fact?
>
> Here's one solution: use leap to create just the "bottom half" of the box,
> which will be filled with water and some ions. Then, edit the last line
> of the inpcrd file you get, making the box twice as long in one direction.
> Voila: you should have a box half-full of salt water and half empty.
>
> Note that, due to periodicity, you will actually have two vacuum-water
> interfaces, one at the "top" of the water, and one at the bottom.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 25 2022 - 18:30:02 PST
