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How to Differentiate Collective Variables in Free Energy Codes: Computer-Algebra Code Generation and Automatic Differentiation
Toni Giorgino
The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instan…
METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations
Toni Giorgino, Alessandro Laio, Alex Rodriguez
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis…
PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts
Toni Giorgino
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take adv…
Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD
Toni Giorgino
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of bio…