Subject: Re: CCL:Trajectory analisys in Hyperchem

From: Mikael Johansson <[email-masked]>
Date: Thu, 19 Oct 2000 13:15:26 +0300 (EET DST)

Hello!

On Wed, 18 Oct 2000, Danilo Gonzalez wrote:

>     I'm working with Hyperchem 5.2 in a PC (Athlon 800 MHz), using AMBER
> force field. I 'm runing a Molecular Dynamics calculation, and saving
> the trayectory file. Anybody know how can I measure the distance between
> two atoms during the trayectory?

You first must select the two atoms you are interested in, and then name
the selection. When starting the MD-run, click on the "Averages..." tab
and move your named selection over to either the "Average only" or "Avg. &
Graph" field. 

After the simulation run you should find a *.csv file with the same base
name that you gave the trajectory file. This should include the distance
between the atoms for each saved time step.

Have a nice day,
    Mikael Johansson
    University of Helsinki
    Department of Chemistry
    [email-masked]