Subject: md simulations/small chunks of proteins

From: Iraj Daizadeh <[email-masked]>
Date: Sat, 22 Jan 2000 13:17:22 -0500 (EST)

Dear Members of the CCL:

Here are some questions that I have been interested in for some time; your
thoughts would be appreciated.

Here's the general problem: Given a alpha helix cut out from a PDB
protein, run md simulations to determine the folling:

1. How can we ensure from md simulations that the alpha helix is stable in
solution?  We solvate the alpha helix the run md simulations for how long?
how much water [10 angstrom solvation shell?]? how many time steps? how
long will the calculation take? and on what machine-- Cray?
etc....details--details--details!

2. References showing that results of the above calculation have been
verified by experiment? References describing results of the above
calculations on such small subsets of PDB data?

I ( as usual ) will post a summary of your responses.

Thanks, Iraj.

Iraj Daizadeh, Ph.D.
Harvard University
Department of Cellular and Molecular Biology
The Biological Laboratories
16 Divinity Avenue
Cambridge, MA 02138
Phone:   (617) 495-0783
         (617) 495-0560
Fax:     (617) 496-4313
Email:   [email-masked]
WebPage: http://mcb.harvard.edu/gilbert/daizadeh