AMBER Archive (2005)

Subject: AMBER: Water simulation

From: David LeBard (david.lebard_at_asu.edu)
Date: Fri Jul 08 2005 - 18:44:12 CDT

Hi All,

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?

This means that I do NOT want to equilibrate the density using NPT
(after temperature equilibration using NVT) then switch back to NVT for
my production run once my density looks okay. Ideally, what I would
like is to simply generate a TIP3P water, replicate it a number of times
until my box of a given size if filled, then melt the replicated system
until it becomes "liquid-like" and run this system for some amount of
time.

Is this even possible in Amber? If not, can any of the developers tell
me some way in which I might programatically change the box length
parameters (for NTB=1) so I have control over my density?

Many thanks in advance,

David LeBard
Dept of Chemistry and Biochemistry
Arizona State University

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