Subject: CCL: VDW collapse

From: Rick Loncharich <[email-masked]>
Date: Fri, 02 Sep 1994 08:31:15 -0500 (EST)

|> From: Hodgkin, Ed
|> 
|> It is well known that molecular mechanics force fields favour 'folded' 
|> conformations which derive stability from large Van Der Waals terms. 
|> One could coin the phrase "Van Der Waals Collapse" to describe this 
|> effect....

|> From: David States
|> . . .  The most direct way to
|> control for the self-association of peptide chains is to do a
|> simulation that includes solvation explicitly.  Note that if you do
|> this as a water droplet rather than a periodic box the internal
|> pressure generated by surface tension is enormous so the system will
|> still collapse some compared to physiologic conditions.

Furthermore, as one increases the amount of water in a water droplet 
simulation from 0 to 4000 water molecules the size of the protein 
(measured by rgyr) increases to the X-ray radius of gyration.  See
recent articles by B.R. Brooks et. al.

Rick Loncharich
Eli Lilly and Company

From: LONCHARICH RICHARD J          (MCVAX0::RX82788)

To:   FOREIGN TRANSPORT ADDRESSEE   (MCDEV1::IN%"[email-masked]")