On 4 Jun 1996 12:39:06 -0700 Gregory King asked:
> 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?
Packages like CHARMM have an improper dihedral energy term which can (and has)
be used to enforce chirality; perhaps increasing the force constants on these
terms during the initial phases of minimization and/or dynamics could prevent
the inversions. It is probably advisable to restore them to the parameter set
values at some point, since otherwise the bond angles are too stiff, etc.
Rick Venable =====\ |=| "Eschew Obfuscation"
FDA/CBER Biophysics Lab |____/ |=|
Bethesda, MD U.S.A. | \ / |=| / Not an official statement \
rvenable at deimos.cber.nih.gov \/ |=| \ or position of the FDA. /