Molecular Utilities

A suite of tools to assist with molecular simulations and analysis.

Contents

• Introduction
• Requirements
• Building the programs

Introduction

This software suite is intended to work with file formats from the Protein data bank (PDB, particularly the fields in an ATOM entry) and the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS, Sandia National Laboratories).

All programs and scripts can be run without command line options for user instructions and example usage.

Documentation for the compiled utilities can be found here, and documentation for the Python utilities can be found here.

Requirements

• Compiler supporting c++11
• Gnu make (or compatible alternative)
• Python (for the PDBTool Python script)

Building the programs

Simply call make in the project directory to build the programs; the binaries are placed into a bin subdirectory.

The fluctuation spectrum analysis program can be compiled to use OpenMP, which could offer a significant performance increase for large wave numbers. This is accomplished bby building the programs with OMP=yes:

make OMP=yes

Note that you may need to change the CC variable if your default compiler does not support OpenMP (e.g. clang on macOS). If you have installed an OpenMP-compliant compiler, specify it as appropriate, e.g.:

make CC=/opt/local/bin/g++-mp-6 OMP=yes

... and you should then have a fluctuation spectrum analysis program with OpenMP acceleration.