AMBER Archive (2005)

Subject: Re: AMBER: Water simulation

From: David LeBard (david.lebard_at_asu.edu)
Date: Sat Jul 09 2005 - 19:30:55 CDT

Prof. Case,

Thank you very much for the help. I definately see why you removed this
option, but it is nice to find that I can change this parameter so
easily still.

Thanks again,

David LeBard
Dept of Chemistry and Biochemistry
Arizona State University

On Fri, 2005-07-08 at 17:13, David A. Case wrote:
> 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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