Re: [AMBER] adding ions to half the water box

From: David A Case <>
Date: Tue, 25 Jan 2022 13:19:28 -0500

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.


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Received on Tue Jan 25 2022 - 10:30:03 PST
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