Paper Citing NAMD - Abstract
Shirvanyants, David; Ding, Feng; Tsao, Douglas; Ramachandran, Srinivas; Dokholyan, Nikolay V.
Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8375-8382, JUL 26 2012
Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force :field by introducing long-range electrostatic interactions to model salt bridges and a sequence dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using small number. of : commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit solvent simulations performed on high end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of. proteins of similar to 100 residues.
