This poster highlights my work on accelerate molecular dynamics in Dr. Andrew McCammon's lab as a graduate student.  First, the method was ported into the ab-initio Car-Parinello molecular dynamics package enableing accelerated quantum mechanical calculations.  Now the method has just been implemented in a QM(CPMD)/MM(GROMOS) context using proton transfer in DHFR as a test system.  Second, the ineffecient implementation of aMD was ported to AMBER10/11 PMEMD allowing much larger and longer aMD simulations to be run.  Third, implementing the method on Nvidia GPU's with Romelia Salomon-Ferrer and Ross Walker.  Finally, several applications will be presented on the following systems DHFR, SH2, SH3, CSK, PKA, cyclotide MCoTI-I, HIV-PR, and BPTI.

Accelerated molecular dynamics: Exploration of the molecular timescale

243rd National Meeting (2012)

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