Subject: Removing charges for an MD simulation

From: [email-masked] (Jeffrey L. Nauss)
Date: Thu, 09 Jan 1997 17:03:29 -0500

One of the problems one has in MD simulations is that long runs must be
performed to see anything significant, for example, and in my specific case,
determination of NMR order parameters or conformational searches.  Performing
the run in explicit solvent with periodic boundary conditions is undoubtably
the best way to perform the simulations.  However, these simulations require
large amounts of CPU time and disk space for the large history files.

To get around these problems, people have run simulations in vacuo.  This was
done in the early days of MD simulations but with parameter sets that often
took into account the absence of solvent.  Furthermore, electrostatic screening
was accomplished by using a distance dependent dielectric constant.  Still, a
continuing problem that I have found during an in vacuo run is the collapse of
the molecule.  Proteins will shrink (in terms of the radius of gyration) and
side chains will fall onto the surface of the protein.  Peptides often fold up
into themselves.  To some extent, this collapse is a result of coulmbic
interactions that are not properly shielded.

Ornstein's group tried to get around this problem by rendering acidic, basic,
N-termini, and C-termini functional groups net neutral (JBSD vol 9, page 935
(1992)).  It appeared to be somewhat successful.

Has anyone tried MD simulations, particularly with small molecules like
peptides and carbohydrates, with a similar approach?   I am thinking perhaps of
performing the simulation with the Coulombic interactions scaled down or even
shut off.  Of course, one must assume that the Coulombic interactions will not
play a major role in the dynamics.  How valid is that assumption will depend on
the system studied, I would think.

Comments will be appreciated.  References will be even better.

-- 
						Jeff Nauss

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*  UU    UU             Jeffrey L. Nauss, PhD                         *
*  UU    UU             Director, Molecular Modeling Services         *
*  UU    UU             Department of Chemistry                       *
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*   UU  UU CCCCCCCC     Cincinnati, OH 45221-0172                     *
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