Main HARLEM Documentation Page

04.02

Abstract

HARLEM (HAmiltonians to Research LargE Molecules) was initially developed as a program to compute electronic donor-acceptor interactions using ab initio Divide-and-Conquer approach but now is gradually evolving to become a multipurpose molecular simulation package with some unique capabilities not to be found in other programs.

Currently the program implements algorithms to compute parameters of long-distance Electron Transfer reactions (donor/acceptor interaction, reorganization energies) in biological and non-biological systems. It also allows (alone and in a combinationation with other programs) to perform Molecular Mechanics, Quantum Chemical and continuum electrostatics calculations of macromolecular systems.

The program has an object oriented design and is written mostly in C++ programming language. I also uses some functions and libraries written in C and FORTRAN. Different computational tasks are performed by separate program modules, organized as C++ classes. This permits easy expandability of the program functionality. The program has a Graphical User Interface (GUI) based on MFC(Microsoft Foundation Classes) and Scripting language interface based on PYTHON. It runs on WINDOWS, LINUX and Digital UNIX ( unix versions run without GUI or using commercial WIN32 porting libraries).

Motivations

Program Intallation

Program Structure

Graphical User Interface

Electron Transfer Rates calculations

Quantum Chemical calculations with HARLEM

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