where stands for the sum of all forces acting on the

While integrating the Newtonian equations of motion computer time is spent mainly on evaluation of the two-particle interactions, i.e., of interactions originating from the Coulomb potential

We have not introduced such a criterion into our
program. Rather than providing a cut-off option we
introduced an option which makes it possible to evaluate the Coulomb interaction
in a hierarchical way such that, according to a hierarchy of inter-particle
distances, Coulomb forces are updated with different frequencies. Such an
algorithm has been suggested in [44] and is
described in [23,21] and in
Section 6.2.1 of this documentation. An alternative
method for an efficient evaluation of Coulomb forces, the *Fast Multipole
Algorithm*, has been developed by Greengard and
Rokhlin [19,20,29] and
is used in EGO simultanously for rapid evaluation of long range forces.
The combination of both algorithms we termed FAMUSAMM.

Calculation of van der Waals and Coulomb forces is the most time consuming task in molecular dynamics calculations. The forces connected with the chemical bonds of biopolymers are determined much more rapidly during program execution. Because of the essentially linear arrangement of biopolymers the respective calculations can be readily ordered in a linear fashion and, therefore, a strategy for parallel computation of forces connected with chemical bonds is straightforward. Hence, we will not explain how these interactions are evaluated. We would like to close this section with a brief description of the input-output requirements of our molecular dynamics program. As input the program needs a file of force parameters, a PDB file of atomic coordinates in protein data bank format, and a PSF protein structure file with definitions of bonds, dihedral and improper angles, etc. The file formats are identical to those of CHARMM and X-PLOR. As output the program delivers atomic coordinates in an internal format which may be converted on the host computer into any format for analysis of trajectory properties by CHARMM, X-PLOR or other programs.

2000-04-19