AMBER Archive (2007)

Subject: Re: AMBER: solvate shell

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Mar 15 2007 - 10:36:52 CST

as far as I know there is no support in amber for doing dynamics with
a solvent shell- you will need to modify the restraint code yourself.
keep in mind that this is an active research area, you should read the
literature about it before trying anything since few studies have been done
and it is not a solved problem.

On 3/15/07, janavi raghavan <genie1080_at_yahoo.co.in> wrote:
>
>
> I am trying to solvate a protein with one layer of
> water.does the solvate shell command in amber perform
> the above operation .does solvateshell need the use of
> non-periodic boundary condition?if so then how do i
> include a code in the input file to restrain the
> surface water molecules only so that it does not
> evaporate.
>
> Thank you in advance
> janavi raghavan
>
>
>
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