ACES Trainee Presentation to the ACES Visiting Committee
Shanadeen Begay
Chemistry Department - Boston University
Thursday - November 29, 2007
Physics Research Building - Room 595

"Extension of Statistical Temperature Molecular Dynamics Algorithm to Include Replica Exchange and All Atom Simulation of Proteins in Explicit Water"

Enhanced sampling techniques are continuously being improved to provide quicker and more accurate conformational sampling of proteins. This work is focused on furthering the implementation of replica exchange statistical temperature molecular dynamics (RE-STMD) into Chemistry HARvard Molecular Mechanics package. Statistical temperature molecular dynamics (STMD) is a promising flat-energy-distribution enhanced sampling method based on molecular dynamics. I will discuss recent implementation and algorithm techniques.