Subject: Hyperchem 3.0

From: [email-masked] ([email-masked])
Date: Mon, 17 Jan 1994 23:32:33 -0500

Hi Joe,
	I am some what familuar with the problem you are having. If you
intend to animate your trajectory you might want to just write out the
coordinates to a file.  You can do this by writing a script to run the
simulation and specify the option: 

notify-on-update coordinates  

there is a sample script in the hyperchem directory react.scr
or this this script I've used in class might help.
-------cut here---------
start-logging hcl_md.log no
append-omsgs-to-file hcl_mdvel.log
open-file hcl_1.hin
render-method spheres
select-atom 1 1
select-atom 2 1
color-selection red
; react.scr
;
; this script is for MD of
; H-Cl
;
; velocity in HIN file is 300 Ansgstroms/picosecond
;
select-none
select-atom 1 1

calculation-method molecularmechanics
molecular-mechanics-method mm+
mechanics-print-level 9
dynamics-restart false
dynamics-run-time 0.2
dynamics-heat-time 0.2
dynamics-cool-time 0
dynamics-time-step 0.0005
dynamics-starting-temp 0.0
dynamics-simulation-temp 300.0
dynamics-temp-step 25
dynamics-constant-temp true
dynamics-snapshot-filename hcl_md.snp
dynamics-snapshot-period 1
dynamics-average-period 20
dynamics-collection-period 20
;velocities 1 1
notify-on-update coordinates
do-molecular-dynamics
query-value velocities
stop-logging
omsgs-not-to-file
exit-script
------------end here-------------------

good luck

Kevin

Kevin McConnell
[email-masked]
Dept. of MB&B
Molecular Biophysics Program
Wesleyan University
Middletown CT.