Subject: Re: CCL:Van Der Waals Collapse

From: [email-masked] (David J. States)
Date: Fri, 2 Sep 1994 07:19:12 -0500

|> 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 the earliest days of charmm development, this has been a concern.
Globular proteins simulated in vacuo shrink when "true" atomic radii
are used as the basis for nonbonded interaction parameters.
Swaminathan spent alot of time working on a compensating force term,
but I don't know what became of the work.  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.

David States

---

From: [email-masked] (Jeffrey L. Nauss)
Date: Fri, 02 Sep 1994 09:11:17 -0400

>From: [email-masked] (David J. States)

>are used as the basis for nonbonded interaction parameters...
>The most direct way to
>simulation that includes solvation explicitly.

I observed this phenomenon when I was running CHARMM a couple years
ago.  However, it does not appear to be a major problem with Biosym's
Discover using the CVFF forcefield.  I emphasis the word major as I do
observe some collapse of proteins and peptides but never to the extent
that CHARMM produced.

Anyone have any comments on the difference between the two forcefields
and this "Van Der Waals Collapse?"  Is anything similar observed with
AMBER or GROMOS?

						Jeff Nauss

****************************************************************************
*  UU    UU             Jeffrey L. Nauss, PhD                              *
*  UU    UU             Director, Molecular Modeling Services              *
*  UU    UU             Department of Chemistry                            *
*  UU    UU CCCCCCC     University of Cincinnati                           *
*   UU  UU CCCCCCCC     Cincinnati, OH 45221-0172                          *
*    UUUU CC                                                               *
*         CC            Telephone: 513-556-0148    Fax: 513-556-9239       *
*         CC                                                               *
*          CCCCCCCC     e-mail: [email-masked]                    *
*           CCCCCCC                                                        *
****************************************************************************