Literature DB >> 30844269

PyLAT: Python LAMMPS Analysis Tools.

Michael T Humbert1, Yong Zhang1, Edward J Maginn1.   

Abstract

Reproducibility and accuracy have become increasingly important issues for the molecular simulation community. The availability of validated open-source postprocessing tools to analyze simulation trajectories and compute properties is key to helping researchers conduct more accurate and reproducible simulations. Here we describe a suite of open-source Python-based postprocessing routines we have developed called PyLAT. PyLAT is compatible with the popular molecular dynamics package LAMMPS and enables users to compute viscosities, self-diffusivities, ionic conductivities, molecule or ion pair lifetimes, dielectric constants, and radial distribution functions using best-practice methods.

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Year:  2019        PMID: 30844269     DOI: 10.1021/acs.jcim.9b00066

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  5 in total

1.  Ionization behavior of nanoporous polyamide membranes.

Authors:  Cody L Ritt; Jay R Werber; Mengyi Wang; Zhongyue Yang; Yumeng Zhao; Heather J Kulik; Menachem Elimelech
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-12       Impact factor: 11.205

Review 2.  Molecular Modeling in Anion Exchange Membrane Research: A Brief Review of Recent Applications.

Authors:  Mirat Karibayev; Sandugash Kalybekkyzy; Yanwei Wang; Almagul Mentbayeva
Journal:  Molecules       Date:  2022-06-02       Impact factor: 4.927

3.  Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solvents.

Authors:  Stephanie Spittle; Derrick Poe; Brian Doherty; Charles Kolodziej; Luke Heroux; Md Ashraful Haque; Henry Squire; Tyler Cosby; Yong Zhang; Carla Fraenza; Sahana Bhattacharyya; Madhusudan Tyagi; Jing Peng; Ramez A Elgammal; Thomas Zawodzinski; Mark Tuckerman; Steve Greenbaum; Burcu Gurkan; Clemens Burda; Mark Dadmun; Edward J Maginn; Joshua Sangoro
Journal:  Nat Commun       Date:  2022-01-11       Impact factor: 14.919

4.  Solubilities and Transport Properties of CO2, Oxalic Acid, and Formic Acid in Mixed Solvents Composed of Deep Eutectic Solvents, Methanol, and Propylene Carbonate.

Authors:  Noura Dawass; Jilles Langeveld; Mahinder Ramdin; Elena Pérez-Gallent; Angel A Villanueva; Erwin J M Giling; Jort Langerak; Leo J P van den Broeke; Thijs J H Vlugt; Othonas A Moultos
Journal:  J Phys Chem B       Date:  2022-05-04       Impact factor: 3.466

5.  Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations.

Authors:  Alper T Celebi; Thijs J H Vlugt; Othonas A Moultos
Journal:  J Phys Chem B       Date:  2019-12-12       Impact factor: 2.991

  5 in total

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