B. Paizs et al., AN EFFICIENT DIRECT METHOD FOR GEOMETRY OPTIMIZATION OF LARGE MOLECULES IN INTERNAL COORDINATES, The Journal of chemical physics, 109(16), 1998, pp. 6571-6576
A new efficient procedure has been developed for geometry optimization
of large molecules using internal coordinates. The method stores only
the nonzero elements of the large transformation matrices, in the spi
rit of direct methods in electronic structure theory. Matrix inversion
has been replaced by iterative solution of linear systems of equation
s by the preconditioned conjugate gradient method. A new incomplete Ch
olesky preconditioner proved essential to accelerate the conjugate gra
dient procedure, The geometries of several alpha helical alanine polyp
eptides, up to 50 alanine units, have been optimized by the new method
, using the SYBYL force field. For larger systems, the number of energ
y/gradient evaluations is reduced by a factor of 6-10, compared to Car
tesian optimization, and the cost of the optimization is small compare
d to the energy calculation, We expect this method to be useful in mol
ecular mechanics and in mixed quantum mechanics/molecular mechanics ca
lculations. (C) 1998 American Institute of Physics. [S0021-9606(98)301
40-3].