Dash logoUC Irvine logo

Simulation input and out and data analysis for calculating partition coefficients of small molecules in octanol/water and cyclohexane/water

Citation

Bannan, Caitlin C; Calabró, Gaetano; Kyu, Daisy Y; Mobley, David L (2016), Simulation input and out and data analysis for calculating partition coefficients of small molecules in octanol/water and cyclohexane/water, Collection, https://doi.org/10.7280/D15K5M

Abstract

Below are summaries for each archived file. There are READMEs in each sub-directory detailing the contents. </p><p> RunFiles.tar These are a set of GROMACS molecular dynamics parameter files and an example run script </p><p> Data.tar.gz This directory contains all data produced by the project including input files created by Solvation Toolkit, output files from the GROMACS simulations, Alchemical Analysis, average density convergence plots, and dictionaries and text files with all calculated and experimental data. </p><p> pythonScripts.tar These are python scripts that were used for the project as a whole. </p><p> ErythromycinConformations.tar This directory contains all the python scripts and analysis related to repeated erythromycin calculations with different initial conformations. </p><p> Density_followup.tar This directory includes python scripts and data analysis for the example density convergence plots that are referenced in the text.

Methods

Associated article is still in review, but we will link it to this database if it is accepted.

Funding

National Institutes of Health, Award: 1R01GM108889-01

National Science Foundation, Award: CHE 1352608 and CHE-0840513