Finding Minima - Conformations, Crystal Polymorphs, and Protein-Peptide Complexes
First procedure to perform a molecular simulation is to make an input, in which a starting geometry (3-dimensional structure) of a molecule or a molecular ensemble must be included. How to design the starting geometry? If you are interesting larger, more flexible, and very complicated molecular system, and if you are expecting the validity of simulation results, it is strongly recommended that some exhaustive search in the potential energy landscape must be preliminarily performed to find every possible geometries, or at least, chemically meaningful geometries.
In this seminar, I will talk about a brief introduction of our computational chemistry system "CONFLEX", that can provide some useful solutions to the problem such as multiple conformations of flexible molecules, polymorphism of molecular crystals,and undetermined binding sites in protein-peptide ligand docking. Performance tests on the parallel computing efficiencies with two supercomputers having different architectures, Xeon vs. SPARC64, will be also presented.