Gregory King wrote:
>> To all practioners of classical molecular mechanics:
>> I've noticed that chiral centers occasionally invert during energy minimization
> or molecular dynamics calculations when a united-atoms representation is used.
>> Have any of you encountered this problem, and if so, what do you do about it?
Chiral inversion is a common problem for united-atom molecular mechanics. A common
solution to the problem (or at least the only solution I know) is to use an
"improper" torsion connecting the atoms neighboring the chiral center. There's a
description of improper torsions in Brooks et al., J. Comput. Chem., 4, 187 (1983).
It will also tell you how to handle the singularities that occur when improper
torsions become planar. This is the original reference for the CHARMm force field,
by the way.
Best regards,
--
Henry Gabb
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX
United Kingdom
