Paper Citing NAMD - Abstract
Muecksch, Christian; Urbassek, Herbert M.
Accelerating Steered Molecular Dynamics: Toward Smaller Velocities in Forced Unfolding Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1380-1384, MAR 2016
The simulation of forced unfolding experiments, in which proteins are pulled apart, is conventionally done using steered molecular dynamics. We present here a hybrid scheme in which accelerated molecular dynamics is used together with steered molecular dynamics. We show that the new scheme changes the force distance curves mainly in the region around the force maximum and thus demonstrate that the improved equilibration of the protein solvent system brought about by using accelerated molecular dynamics makes the simulation more comparable to experimental data.
