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ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program calculates the solvation free energy in arbitrary solvent, including inhomogeneous system, without requiring tuning parameters for specific solvent species. It can run in cooperation with state-of-art molecular simulation softwares, such as LAMMPS, GROMACS and/or AMBER.

Quick Start Guide

• New to ERmod? Please read this guide first!

Parameters

• Parameter files for erdst
• Parameter files for slvfe
• Parameter files for ermod (ver 0.2)

Outputs from erdst run

Build Guide

• General build guide
• Build guides for supercomputers
• VMD plugin build
• Build guide on Mac OS X
• Build guide on Windows Subsystem for Linux
• Build guide on Cygwin

TIPS

• Practices for a single-molecule simulation of isolated solute
• Assessing the convergence with respect to the reference-solvent calculation
• Sampling interval of MD
• Debugging practice for the reference-solvent calculation
• To read a trajectory format which is not supported in VMD plugins

Advanced Guides

• Lennard-Jones long-range correction
• Finite concentration of solute: when more than one molecules are present for the solute species
• Running integral over the energy coordinate, and the estimation of the excluded-volume contribution
• Free energy calculation of protein solvation with explicit solvent
• Ligand-binding into protein at fixed ligand-protein configuration
• Generating EcdInfo semi-automatically
• Reducing the computation time for slvfe
• How to use mol_dissect (ver 0.3)

FAQ

• Frequently asked questions at the installation
• Frequently asked questions at running the erdst program
• Handling output files
• Error in gen_structure: IndexError: list index out of range
• Error in erdst: The minimum of the energy coordinate is too large
• Error in slvfe: Incorrect normalization at (integer value)
• Warning in slvfe: mesh error is (real value1) kcal/mol and is larger than the recommended value of (real value2) kcal/mol

Mailing List and Support

• Mailing List and Support Page

Migration Guides

• Migration from 0.3 to 1.0
• Migration from 0.2 to 0.3
• Migration from 0.1 to 0.2

Benchmarks

Performance information will be posted here.

Technical & Theoretical Documents

• Lecture Notes
• Theories
• Technical Notes
• Developer's Guide