title: Project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model"
author: Raffaele Fiorentini
description: README file for the project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model" February 12, 2020 Authors: Raffaele Fiorentini, Kurt Kremer and Raffaello Potestio ================================ Overview The dataset is organised in three (compressed) subfolders (see the tree diagrams in each section): - annihilation - decoupling - density The figure deltaG_binding_ann_dec_comparison.png shows the results of binding free energy calculations comparing the values obtained both for annihilation and decoupling. The figure deltaG_binding_annih_gromacs_espp.png displays the results for Binding FE, comparing the values obtained in GROMACS and ESPResSo++. The README.pdf file contains detailed information about these folders and their content. ================================ The "annihilation" folder contains all results concerning the calculation of binding free energy in case of annihilation and it is divided in two parts:  - complex - ligand In "complex" are reported the results of Ligand-Protein FE both in ESPResSo++ and GROMACS. All simulations are fully-atomistic.  In "ligand" are reported the results of ligand solvation free energy both in ESPResSo++ and GROMACS. All simulations are fully-atomistic.  ==== The "decoupling" folder contains all results concerning the calculation of binding free energy in case of decoupling and it is divided in three parts:  - complex-DualRes - complex-FullyAT - ligand In "complex-DualRes" are reported the results of Ligand-Protein FE only in ESPResSo++ (GROMACS cannot do decoupling). The system is simulated in Dual-Resolution. It is possible to find the trajectory files in the sub-directories "lambdaindex-0" and "lambdaindex-30". In "complex-fullyAT" are reported the results of Ligand-Protein FE only in ESPResSo++. The system simulated is fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-30". In "ligand" are reported the results of ligand solvation free energy only in ESPResSo++. All simulations are fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-20". ==== The "density" folder contains the data for the tuning of the c parameter of the steric repulsion among residues. This parameter is tuned so that the water density attains the value computed in all-atom simulations.