AMBER Archive (2008)

Subject: Re: AMBER: How to set up a water slab in Amber?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Oct 01 2008 - 06:51:17 CDT

On Tue, Sep 30, 2008, Zhao, Zhen (zhaozh) wrote:
>
> I want to set up a water slab in Amber. For example, I want the system to be
> periodic in both x and y directions , but not the z direction.
> Does anyone know how to do this in Amber? It seems that the keyword "ntb"
> has only three options(no periodic, periodic with constant
> volume and periodic with constant pressure). Thanks in advance!

What you want is not directly supported in Amber. You could try a fully
periodic system, but just have a long z-axis and a large gap between images in
that direction.

...good luck...dac

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