AMBER Archive (2005)

Subject: Re: AMBER: Water simulation

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 08 2005 - 19:13:37 CDT

On Fri, Jul 08, 2005, David LeBard wrote:
>
> I would like to run a production NVT simulation of TIP3P water at a
> given density (rho) that is temperature dependent according to the
> volume expansion coefficient (alpha). If I know the number of waters in
> my simulation, is there any way I can change my lengths of my box to fit
> a particular rho?

If your density is not too far away from realistic water densities, you can
just manually edit the last line of the restart files, which contains the box
dimensions. Then, if you continue with NVT dynamics, you will have the
desired volume (and hence, the desired density).

(Earlier versions of Amber allowed users to enter the box dimenions in the
input file. But in practice, this led to lots of mistakes when people
re-used old input files and forgot to change the box information.)

...good luck...dac

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