Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

(2016) Josh V. Vermaas et al.   Journal of Chemical Information and Modeling

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular containers assembled through the hydrophobic effect

(2015) Jacobs H. Jordan et al.   CHEMICAL SOCIETY REVIEWS

Direct-Space Corrections Enable Fast and Accurate Lorentz–Berthelot Combination Rule Lennard-Jones Lattice Summation

(2015) Christian L. Wennberg et al.   Journal of Chemical Theory and Computation

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

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

(2014) Jacob I. Monroe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Acyclic Cucurbit[n]uril-type Molecular Containers: Influence of Aromatic Walls on their Function as Solubilizing Excipients for Insoluble Drugs

(2014) Ben Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Guest-mediated switching of the assembly state of a water-soluble deep-cavity cavitand

(2013) Haiying Gan et al.   CHEMICAL COMMUNICATIONS

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions

(2013) Himanshu Paliwal et al.   Journal of Chemical Theory and Computation

Binding of cyclic carboxylates to octa-acid deep-cavity cavitand

(2013) Corinne L. D. Gibb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL2 blind prediction challenge: introduction and overview

(2010) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software

(2009) Michael F. Crowley et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

(2009) J. Peter Guthrie   JOURNAL OF PHYSICAL CHEMISTRY B

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

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