AMBER Archive (2003)

Subject: Re: script for Potential/kinectic energy

From: Luis Gracia (luis.gracia_at_mssm.edu)
Date: Mon Jan 20 2003 - 12:16:52 CST

Layi Adekoya wrote:
> Hi,
> Please does anyone has a script that
> can extract energies from MD output file
> that will calculate a ratio of
> Kinetic/Potential energy.I want
> to use it to plot this ratio
> against time in ps for my MD run.
> AMBER7 format. Thanks
>
> Looking forward to hearing from you.
>
> Layi
>

Hi, I have a script that extracts the info from a minimization or md
run, from the .out and .mden files (amber 6 and amber 7, and namd
2.5b1), and using gnuplot automatically gives the plot. You can find a
version in http://plotamber.sf.net.
It does not plot the ratio you are asking for, but can save a file with
all the data in column file, which you can import to any graphics program.

Best,

Luis 

-- 
Luis Gracia, PhD
Dept. Physiology & Biophysics, 21-280
Mt Sinai School of Medicine
One Gustave L. Levy Place, New York NY 10029
Tel: (212) 241-0858   ---   Fax: (212) 860-3369
e.mail: luis.gracia_at_mssm.edu