Paper Citing NAMD - Abstract
Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto
Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4837-4844, NOV 2012
The nonequilibrium stretching of decaalanine in vacuum using steered molecular dynamics and Jarzynski's relation led to the landmark determination of its potential of mean force by Park and Schulten (Chem. Phys. 2004). In so doing, the relative thermodynamics of the hydrogen-bond contacts and the entropy of the chain were quantified through the reversible work, the potential of mean force (PMF). A recently developed adaptive steered molecular dynamics algorithm (Ozer et al. J. Chem. Theory Comput. 2010) has now made it possible to determine the thermodynamics, PMF, of the stretching of decaalanine in a model solvent of TIP3P water molecules. The loss of internal hydrogen bonds and the formation of hydrogen bonds between the peptide and the solvent has also been tracked with the corresponding stabilization in the PMF. As in the vacuum, most of the thermodynamic penalty to unravel the chain in solvent occurs during the regime when the internal hydrogen bonds are broken. The formation of hydrogen bonds with the solvent provides a significant stabilization not seen in vacuum, reducing the total energy cost to unravel by nearly a factor of 2.
