Paper Citing NAMD - Abstract
Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto
Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 215104, JUN 7 2012
The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i --> i + 4 contacts (alpha-helix) is replaced by i --> i + 3 contacts (3(10)-helix). No significant formation of i --> i + 5 hydrogen bonds (pi-helix) is observed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4725183]
