GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

(2016) Lu Zhang et al.   ACCOUNTS OF CHEMICAL RESEARCH

Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

(2016) Jaewoon Jung et al.   COMPUTER PHYSICS COMMUNICATIONS

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Advances in free-energy-based simulations of protein folding and ligand binding

(2016) Alberto Perez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations

(2016) Jaewoon Jung et al.   Journal of Chemical Theory and Computation

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein

(2016) Yasuhiro Matsunaga et al.   Journal of Physical Chemistry Letters

Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions

(2016) Kshitij Khatri et al.   MOLECULAR & CELLULAR PROTEOMICS

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Parameters for Martini sterols and hopanoids based on a virtual-site description

(2015) M. N. Melo et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

(2015) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins

(2015) Chigusa Kobayashi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

(2015) Jaewoon Jung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Effects of truncating van der Waals interactions in lipid bilayer simulations

(2014) Kun Huang et al.   JOURNAL OF CHEMICAL PHYSICS

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

(2014) Y. Andoh et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison between Mean Forces and Swarms-of-Trajectories String Methods

(2014) Luca Maragliano et al.   Journal of Chemical Theory and Computation

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations

(2014) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics

(2014) Fan Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

(2013) Wei Jiang et al.   COMPUTER PHYSICS COMMUNICATIONS

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

(2013) Ross A. Lippert et al.   JOURNAL OF CHEMICAL PHYSICS

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems

(2013) Takaharu Mori et al.   Journal of Chemical Theory and Computation

MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms

(2013) Yoshimichi Andoh et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Efficient lookup table using a linear function of inverse distance squared

(2013) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

(2013) Pai-Chi Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

(2013) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Computational studies of molecular machines: the ribosome

(2012) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles

(2012) Michael R. Shirts   Journal of Chemical Theory and Computation

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Replica-exchange molecular dynamics simulation of a lipid bilayer system with a coarse-grained model

(2011) Tetsuro Nagai et al.   MOLECULAR SIMULATION

Multiscale Computer Simulation of the Immature HIV-1 Virion

(2010) Gary S. Ayton et al.   BIOPHYSICAL JOURNAL

Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-Grained Analysis

(2010) Vinod Krishna et al.   BIOPHYSICAL JOURNAL

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Presentation of Membrane-Anchored Glycosphingolipids Determined from Molecular Dynamics Simulations and NMR Paramagnetic Relaxation Rate Enhancement

(2010) Mari L. DeMarco et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations

(2010) Y. Sugita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tofu: A 6D Mesh/Torus Interconnect for Exascale Computers

(2009) Yuichiro Ajima et al.   COMPUTER

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

(2009) Giovanni Bussi et al.   JOURNAL OF CHEMICAL PHYSICS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

A new force field for simulating phosphatidylcholine bilayers

(2009) David Poger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations

(2009) Naoyuki Miyashita et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces

(2008) M. L DeMarco et al.   GLYCOBIOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids

(2008) M.B. Tessier et al.   MOLECULAR SIMULATION

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE