Kim, Seonah; Roitberg, Adrian E.. Simulating Temperature Jumps for Protein Folding
Journal of Physical Chemistry B, 2008-01-15
Abstract: We present a new computational methodology aimed to calculate the thermodynamics and kinetics of peptide folding. We focus in particular on temperature jump experiments of folding rates and show how a combination of replica exchange molecular dynamics (REMD) followed by multiplexed molecular dynamics starting from structures taken from the REMD runs can be used to extract properties in line with experiments. A model system, alanine20, is studied in this article as a proof of principle and used to describe the methodology.