From chemistry-request@ccl.net Thu Mar 12 11:46:25 1992
Date: Thu, 12 Mar 92 09:00:50 CST
From: ssidner@unmc.EDU (Steve Sidner)
Subject: Re:  A question for Mac users
To: chemistry@ccl.net
Status: R

In regards:
	Fellow Netters,

	    This is a question for all you Mac users.  Is there a Mac
	    program out there that will take a post script file and
	render a picture on the screen that one can cut and paste?  Our
	graphics codes produce post script files for hard copies but it
	would be nice to edit the pictures on the Mac before printing.
	Any held will be greatly appreciated.

				     Jan H. Jensen Dept. of Chemistry
				     North Dakota State University
				     Fargo, ND 58105

A cheap and dirty way is using Aldus SuperPaint 3.0.  You can place EPS
files into the draw layer of a new document, cut it to the paint layer,
and then go from there.

Steve Sidner
Eppley Institute
University of Nebraska Medical Center
Omaha, Nebraska


----- End Included Message -----


From chemistry-request@ccl.net Thu Mar 12 14:12:14 1992
Date: Thu, 12 Mar 1992 11:23 CST
From: CMSWALTERS@minna.iit.EDU
Subject: CD-ROM advice?
To: chemistry@ccl.net
Status: R

Looking for some advice.  I need to get a CD-ROM for occasional use
on my SGI [like loading system software].  I also would like to use
a CD-ROM occasionally on a Macintosh.  Can I get one CD-ROM drive
which will work on both systems, or am I doomed to buy two different
drives?  I don't mind if I have to disconnect/connect in order to 
switch between machines, but I'd like to get one device that will
be usable on both systems.  Thanks!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> D. Eric Walters                                                         >
> Assoc. Prof. Biological Chemistry                                       >
> Chicago Medical School                phone: 708-578-3000, ext 498      >
> 3333 Green Bay Road                   fax: 708-578-3240                 >
> North Chicago, IL  60064              email: cmswalters@minna.iit.edu   >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

From jkl@ccl.net Thu Mar 12 14:35:07 1992
To: chemistry@ccl.net
Subject: Time step in MD
Date: Thu, 12 Mar 92 14:35:01 EST
From: jkl@ccl.net
Status: R

The discussion on the cutoff distances and time steps is very stimulating.
However, I do not understand something here. 
The time step chosen in Molecular Dynamics is for me a purely mathematical
parameter affecting the precision of integration, but not the physics of the
simulated system. If we had computers with infinite precision and infinite
speed, we should use the small integration step (e.g., 1.0E-20 s). But
our machines have final floating point precision and we cannot go too small
or the truncation errors will add up substantially. Also the machines of
today are slow, and we would not get results in our lifetime.
On the other hand, choosing the integration step too large would result in
errors in integration (like numerically integrating the sin function
with a step of 180 degrees) and would produce wrong trajectories.
For me, time step in MD is mathematics, not physics, like choosing
the grid size in numeric Hartree-Fock atomic calculations:
the smaller the better, and the smaller is much below Heisenberg principle.

However, with Monte Carlo, I do not know how small the amplitude of the
random generator could be in Angstroms before we violate something.
Maybe here the Heisenberg principle is applicable, but I sincerely doubt.
We are also probing the energy surface with a mathematical tool.

Jan Labanowski
Ohio Supercomputer Center
jkl@ccl.net