Glossary

Key Points

Introduction: Basic introduction to MD	bad systems into the engeine give bad data out For every step of the system the total ponteial energy is found that is the sum of the forces on each atom
Using Nanoscale Molecular Dynamics (NAMD) on WVU HPC resources	Globus Connect is the best way to transfer files to the HPC. Use a pbs script to submit jobs to the cluster. Perform benchmarking to get the most out of your resources.
Using Gromacs on WVU HPC resources
Using AMBER on WVU HPC resources	Sander is used for simualtions that require changes in the periodic box The GPU code for amber is run on the GPU and needs only one cpu for commincation to run optimally

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