Design of a modular Fortran 90 molecular mechanics package for hydrocarbons

Shaw, Michelle (2000) Design of a modular Fortran 90 molecular mechanics package for hydrocarbons. Masters thesis, Memorial University of Newfoundland.

[English] PDF (Migrated (PDF/A Conversion) from original format: (application/pdf)) - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. Download (16MB) [English] PDF - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. (Original Version)

Abstract

Molecular mechanics is a popular method for minimization of energies of large biomolecular structures and much work has been done in creating packages which optimize the execution time and memory requirements. Object-based design is a useful tool in creating packages which are easily updated and clearer than procedural-based design due to their inherent modularity. The current codes in use are Fortran 77 and C, but Fortran 90 may prove to be a more viable option for object-based molecular mechanics. In this work, a molecular mechanics package based on the Merck Molecular Force Field (MMFF94) is designed for hydrocarbons using existing Fortran 90 tools and object-based design techniques. Presented in this work are the analysis, design, and implementation of the molecular mechanics package as well as a report of the numerical results. Included in the numerical results are comparisons with literature values for the conformational differences for the ethane and cyclohexane systems.

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