Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Gaussian Accelerated Molecular Dynamics in OpenMM

Journal Article · · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

Not provided.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC02-05CH11231
OSTI ID:
1981901
Journal Information:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Vol. 126, Issue 31; ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English

References (71)

Molecular dynamics simulations of biomolecules journal September 2002
Molecular Dynamics Simulation for All journal September 2018
Dynamic personalities of proteins journal December 2007
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale journal May 2009
Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors journal August 2011
Atomic-Level Characterization of the Structural Dynamics of Proteins journal October 2010
To milliseconds and beyond: challenges in the simulation of protein folding journal February 2013
Measurement of the millisecond activation switch of G protein–coupled receptors in living cells journal June 2003
Viral structural transitions: An all-atom multiscale theory journal December 2006
Enhanced sampling techniques in biomolecular simulations journal November 2015
Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems journal April 2008
Computational techniques for efficient conformational sampling of proteins journal April 2008
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review journal January 2007
Unconstrained enhanced sampling for free energy calculations of biomolecules: a review journal July 2016
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling journal February 1977
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method journal October 1992
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science journal November 2008
Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions book November 2011
Adaptive biasing force method for scalar and vector free energy calculations journal April 2008
Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm journal January 2002
Steered molecular dynamics investigations of protein function journal February 2001
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations journal May 2004
Parallel tempering algorithm for conformational studies of biological molecules journal December 1997
Self-guided Langevin dynamics simulation method journal November 2003
Self-guided Langevin dynamics via generalized Langevin equation journal July 2015
Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search journal August 1998
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules journal June 2004
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events journal May 1997
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation journal July 2015
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation journal May 2014
Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor journal April 2021
Mechanism of Ligand Recognition by Human ACE2 Receptor journal May 2021
Gaussian Accelerated Molecular Dynamics in NAMD journal December 2016
Recognition of single-stranded nucleic acids by small-molecule splicing modulators journal July 2021
GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling journal February 2022
Mechanisms of γ-Secretase Activation and Substrate Processing journal June 2020
Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase journal April 2022
Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor journal October 2016
G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State journal October 2019
Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor journal March 2018
Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors journal July 2019
Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics journal January 2022
Allosteric Motions of the CRISPR–Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics journal December 2019
Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics journal March 2019
Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation journal February 2018
Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules journal September 2019
Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics journal July 2020
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding journal October 2020
An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems journal January 2022
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation journal November 2012
Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units journal October 2013
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born journal April 2012
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald journal August 2013
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package
  • Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2 https://doi.org/10.1002/wcms.1121
journal September 2012
Comparison of simple potential functions for simulating liquid water journal July 1983
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles journal August 2011
A fast and high-quality charge model for the next generation general AMBER force field journal September 2020
The crystal structure of UUCG tetraloop 1 1Edited by J Doudna journal November 2000
A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops journal December 1996
Solution Structure of the CUUG Hairpin Loop: A Novel RNA Tetraloop Motif journal November 1995
Rational Design of Inhibitors of HIV-1 TAR RNA through the Stabilisation of Electrostatic “Hot Spots” journal February 2004
CHARMM-GUI: A web-based graphical user interface for CHARMM journal March 2008
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field journal December 2015
CHARMM-GUI supports the Amber force fields journal July 2020
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes journal March 1977
Molecular dynamics with coupling to an external bath journal October 1984
A smooth particle mesh Ewald method journal November 1995
VMD: Visual molecular dynamics journal February 1996
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data journal June 2013
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations journal September 2013
Reaction Coordinate and Thermodynamics of Base Flipping in RNA journal February 2021