CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

(2021) Krishan Kanhaiya et al.   npj Computational Materials

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

(2021) Yeol Kyo Choi et al.   Journal of Chemical Theory and Computation

MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films

(2020) Andrew Z. Summers et al.   Journal of Chemical Theory and Computation

Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations

(2020) Xiliang Yan et al.   Nature Communications

Understanding the Surface Reactivity of Ligand-Protected Metal Nanoparticles for Biomass Upgrading

(2020) Lesli O. Mark et al.   ACS Catalysis

CHARMM-GUI supports the Amber force fields

(2020) Jumin Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Force field for calcium sulfate minerals to predict structural, hydration, and interfacial properties

(2020) Ratan K. Mishra et al.   CEMENT AND CONCRETE RESEARCH

NanoMaterialsCAD: Flexible Software for the Design of Nanostructures

(2020) Giorgos Nikoulis et al.   Advanced Theory and Simulations

NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles

(2019) Sebastian Franco-Ulloa et al.   Journal of Chemical Theory and Computation

Carbon nanotube bundles with tensile strength over 80 GPa

(2018) Yunxiang Bai et al.   Nature Nanotechnology

Two-dimensional semiconductors in the regime of strong light-matter coupling

(2018) Christian Schneider et al.   Nature Communications

Tinker 8: Software Tools for Molecular Design

(2018) Joshua A. Rackers et al.   Journal of Chemical Theory and Computation

Formation of nanopores in DiynePC–DPPC complex lipid bilayers triggered by on-demand photo-polymerization

(2018) Min Jung Chun et al.   RSC Advances

Building two-dimensional materials one row at a time: Avoiding the nucleation barrier

(2018) Jiajun Chen et al.   SCIENCE

A force-matching Stillinger-Weber potential for MoS2: Parameterization and Fisher information theory based sensitivity analysis

(2017) Mingjian Wen et al.   JOURNAL OF APPLIED PHYSICS

Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom

(2017) Michael Schappals et al.   Journal of Chemical Theory and Computation

The atomic simulation environment—a Python library for working with atoms

(2017) Ask Hjorth Larsen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Deciphering chemical order/disorder and material properties at the single-atom level

(2017) Yongsoo Yang et al.   NATURE

Abiotic tooth enamel

(2017) Bongjun Yeom et al.   NATURE

Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

(2017) Hendrik Heinz et al.   SURFACE SCIENCE REPORTS

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Simulations of inorganic–bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

(2016) Hendrik Heinz et al.   CHEMICAL SOCIETY REVIEWS

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces

(2016) Tzu-Jen Lin et al.   Journal of Physical Chemistry C

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

(2016) Jing Huang et al.   NATURE METHODS

Surface energies of elemental crystals

(2016) Richard Tran et al.   Scientific Data

Molecular Mechanism of Specific Recognition of Cubic Pt Nanocrystals by Peptides and of the Concentration-Dependent Formation from Seed Crystals

(2015) Hadi Ramezani-Dakhel et al.   ADVANCED FUNCTIONAL MATERIALS

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

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

Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution

(2014) Fateme S. Emami et al.   CHEMISTRY OF MATERIALS

A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

(2014) Ratan K. Mishra et al.   DALTON TRANSACTIONS

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computer simulations of fibronectin adsorption on hydroxyapatite surfaces

(2014) Chenyi Liao et al.   RSC Advances

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Force Field for Tricalcium Silicate and Insight into Nanoscale Properties: Cleavage, Initial Hydration, and Adsorption of Organic Molecules

(2013) Ratan K. Mishra et al.   Journal of Physical Chemistry C

Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field

(2013) Hendrik Heinz et al.   LANGMUIR

Clay minerals for nanocomposites and biotechnology: surface modification, dynamics and responses to stimuli

(2012) H. Heinz   CLAY MINERALS

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

Molecular Dynamics Simulations of Structural and Mechanical Properties of Muscovite: Pressure and Temperature Effects

(2012) Stephanie L. Teich-McGoldrick et al.   Journal of Physical Chemistry C

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

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

The potential of atomistic simulations and the knowledgebase of interatomic models

(2011) E. B. Tadmor et al.   JOM

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

The Dissociated Amorphous Silica Surface: Model Development and Evaluation

(2010) Ali A. Hassanali et al.   Journal of Chemical Theory and Computation

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

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simple application of fibronectin-mimetic coating enhances osseointegration of titanium implants

(2008) Timothy A. Petrie et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials

(2008) Hendrik Heinz et al.   Journal of Physical Chemistry C