Molecular Simulation Timeline - Concepedia

Concepedia

Concept

molecular simulation

Parents

Biomolecular Engineering

27.1K

Publications

2.3M

Citations

49.2K

Authors

5.7K

Institutions

Ensemble-Driven Molecular Dynamics

1962 - 2024

Molecular simulation matured into ensemble-based sampling with robust thermostatting and external-bath coupling that sustains long biomolecular trajectories. Time-scale aware strategies combined multi-time-scale integration with constraint solving to accelerate large systems while preserving stability. Free-energy and sampling frameworks matured, including methods for estimating free-energy landscapes and ensemble analyses that enable reliable thermodynamic inferences. Biomolecular force fields and energy models advanced across all-atom representations and parameter reparameterization, with versatile energy functions for proteins and nucleic acids. Software ecosystems standardized MD workflows, with widely adopted platform tools and trajectory-analysis pipelines shaping daily practice.

• Molecular dynamics (MD) work consolidated around robust ensemble control, establishing constant temperature and/or pressure simulations, external-bath coupling, and unified thermostatting frameworks to sustain long trajectories [3] [2] [14] [20].

• Time-scale aware simulation paradigms emerged, combining multi-time-scale integration with robust constraint solving to accelerate large biomolecular simulations while maintaining stability [4] [13] [9].

• Free-energy and sampling frameworks matured, including the Weighted Histogram Analysis Method for biomolecules and ensemble/phase-coexistence approaches that enable robust thermodynamic inferences [5] [18] [19].

• Biomolecular force fields and energy models advanced, spanning all-atom force fields, parameter reparameterization, and versatile energy functions used for proteins and nucleic acids [8] [7] [16].

• Software ecosystems and platform-level MD tools standardized workflows, with prominent role of macromolecular modeling packages and trajectory-analysis platforms exemplified by CHARMm and GROMACS [1] [15].

Popular Keywords

molecular dynamics

computational chemistry

physical chemistry

[1]

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling

[2]

Molecular dynamics with coupling to an external bath

1984 • biophysics, computational chemistry, molecular dynamics, molecular kinetics, molecular mechanic, physical chemistry

[3]

Molecular dynamics simulations at constant pressure and/or temperature

1980 • biophysics, computational chemistry, molecular dynamics, molecular kinetics

[4]

Reversible multiple time scale molecular dynamics

1992 • biophysics, computational biochemistry, computational chemistry, molecular dynamics

[5]

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

1992 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling

[6]

Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen

1989 • computational biochemistry, computational chemistry, quantum chemistry

[7]

Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides

2001 • biophysics, computational biochemistry, computational chemistry, molecular mechanic, molecular modeling

[8]

An all atom force field for simulations of proteins and nucleic acids

1986 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic

[9]

New spherical‐cutoff methods for long‐range forces in macromolecular simulation

1994 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling

[10]

Improved simulation of liquid water by molecular dynamics

1974 • chemical thermodynamics, computational chemistry, molecular dynamics, molecular mechanic, quantum chemistry

[11]

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

2000 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling, physical chemistry, quantum chemistry

[12]

CI study of the water dimer potential surface

1976 • biophysics, chemical thermodynamics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, physical chemistry, quantum chemistry

[13]

LINCS: A linear constraint solver for molecular simulations

1997 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling

[14]

A unified formulation of the constant temperature molecular dynamics methods

1984 • biophysics, chemical thermodynamics, computational chemistry, molecular dynamics, molecular kinetics, molecular mechanic, physical chemistry, quantum chemistry

[15]

GROMACS 3.0: a package for molecular simulation and trajectory analysis

2001 • biophysics, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling

[16]

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

1992 • biophysics, computational chemistry, molecular dynamics, molecular mechanic, molecular modeling, physical chemistry, quantum chemistry

[17]

A generalized reaction field method for molecular dynamics simulations

1995 • biophysics, computational chemistry, molecular dynamics, molecular kinetics, molecular mechanic, molecular modeling, quantum chemistry

[18]

Configurational bias Monte Carlo: a new sampling scheme for flexible chains

1992 • biophysics, computational chemistry, molecular dynamics

[19]

Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble

2002 • biophysics, computational chemistry

[20]

Constant pressure molecular dynamics simulation: The Langevin piston method

1995 • biophysics, computational biochemistry, computational chemistry, molecular dynamics, molecular kinetics, molecular mechanic