pysimm: A python package for simulation of molecular systems

Plimpton, 1995, Fast parallel algorithms for short-range molecular dynamics, J Comput Phys, 117, 1, 10.1006/jcph.1995.1039 Case, 2016 Abraham, 2015, Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX 1–2, 19, 10.1016/j.softx.2015.06.001 Brooks, 2009, Charmm: The biomolecular simulation program, J Comput Chem, 30, 1545, 10.1002/jcc.21287 Anderson, 2008, General purpose molecular dynamics simulations fully implemented on graphics processing units, J Comput Phys, 227, 5342, 10.1016/j.jcp.2008.01.047 Eastman, 2013, Openmm 4: A reusable, extensible, hardware independent library for high performance molecular simulation, J Chem Theory Comput, 9, 461, 10.1021/ct300857j Shah, 2011, A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules, J Chem Phys, 135, 134121, 10.1063/1.3644939 Martínez, 2009, PACKMOL: A package for building initial configurations for molecular dynamics simulations, J Comput Chem, 30, 2157, 10.1002/jcc.21224 Klein, 2016, A Hierarchical, Component Based Approach to Screening Properties of Soft Matter, 79, 10.1007/978-981-10-1128-3_5 Landrum G. Rdkit: Open-source cheminformatics. Accessed 8 August 2016. O’Boyle, 2011, Open Babel: An open chemical toolbox, J Chem Inf, 3, 1 Sarkisov, 2011, Computational structure characterisation tools in application to ordered and disordered porous materials, Mol Simul, 37, 1248, 10.1080/08927022.2011.592832 Humphrey, 1996, VMD: Visual Molecular Dynamics, J Mol Graph, 14, 33, 10.1016/0263-7855(96)00018-5 Schrödinger, LLC, The PyMOL molecular graphics system, version 1.8, 2015. McGibbon, 2015, Mdtraj: A modern open library for the analysis of molecular dynamics trajectories, Biophys J, 109, 1528, 10.1016/j.bpj.2015.08.015 Haley BP, Wilson N, Li C, Arguelles A, Jaramillo E, Strachan A. Polymer modeler, Aug 2016. http://dx.doi.org/10.4231/D3X921K69, URL https://nanohub.org/resources/9230. Abbott L, Colina C. Polymatic: A simulated polymerization algorithm, Mar 2016. URL https://nanohub.org/resources/17278. Degiacomi, 2016, Easy creation of polymeric systems for molecular dynamics with assemble!, Comput Phys Comm, 202, 304, 10.1016/j.cpc.2015.12.026 Fortunato M, Abbott L, Hart KE, Colina C. nusimm: nanohub user simulation interface for molecular modeling (2016), http://dx.doi.org/10.4231/D3ZP3W18X, URL https://nanohub.org/resources/22366. Madhavan, 2013, nanohub.org: Cloud-based services for nanoscale modeling, simulation, and education, Nanotechnology Rev, 2, 107, 10.1515/ntrev-2012-0043 Abbott, 2013, Polymatic: a generalized simulated polymerization algorithm for amorphous polymers, Theoret Chem Acc, 132, 1, 10.1007/s00214-013-1334-z iChemLabs LLC. Chemdoodle web components. Accessed 8 August 2016.