Understanding Molecular Simulation

By D. Frenkel, Berend Smit. 2001

6,222 citations recorded by the source corpus.

Subfields: Molecular Biology, Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Computational Chemistry & Drug Discovery

Citations in the corpus

Stochastic Normalizing Flows (2020, methodology): “For sampling energy-based models, an alternative to ﬂows is to use Markov Chain Monte Carlo (MCMC) or other stochastic sampling methods (Frenkel & Smit, 2001).”
Molecular dynamics simulations of glassy polymers (2010, background): “Sections 3 and 4 will present results from molecular dynamics (MD) simulations, a numerical method to integ rate the classical equations of motion for a many-body system in a given thermodynam ic ensemble [68, 69].”
Fluid and solid phases of the Gaussian core model (2000, methodology): “urse also possible to calculate the exact free energies of the various candidate phases in a simulation, by means, e.g., of the virial route in the ﬂuid state and by employing the Frenkel-Ladd method [3, 4, 8, 45, 46] in the solid state. However, the latter is very time-consuming. The very good agre”
Prediction of the material with highest known melting point from ab initio molecular dynamics calculations (2015, methodology): “[20] D.”
Composition and temperature of the Earth's core constrained by combining ab initio calculations and seismic data (2002, methodology): “For the liquid, this vF is computed by applying the technique of `thermodynamic integration' [23] to the (hypothetical) process in which an Fe atom is continuously transmuted into an X atom, as described in [6].”
Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, background): “For Cartesian CVs, the correction vanishes and the mean forces can be calculated as the negative of the time average of the constraint forces in a constrained MD simulation [4].”
Guidelines for the analysis of free energy calculations (2015, methodology): “In principle, free energy differences between the end states can be computed simply from simulations conducted in one or both states [11].”