ABSTRACT:    Molecular dynamics (MD) simulation provides a powerful tool to study molecular motion with respect to classical mechanics. When considering protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds.  To date, literature reports simulations of solvated proteins on the order of nanoseconds, however, simulations of this length do not provide adequate sampling for the study of large-scale molecular motion.


In this presentation I will describe a method for performing molecular simulations with respect to a reduced coordinate space. Given a standard MD trajectory I use principal component analysis to identify k dominant characteristics of a trajectory and construct a k-dimensional (k-D) representation of the atomic coordinates with respect to these k characteristics.  Using this model I define equations of motion and perform simulations with respect to the constructed k-D representation. I apply this reduced basis simulation method to test cases and compare the simulations to standard MD simulations of the test cases.  The results indicate that the molecular activity with respect to the reduced basis simulation method is comparable to that observed in the standard MD simulations of test cases.