Bottom-up Open-source Coarse-graining Software
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README.md

README.md

BOCS

Bottom-up Open-source Coarse-graining Software (BOCS, pronounced 'box') is software for parameterizing thermodynamically accurate and transferable bottom-up coarse-grained (CG) force fields. This software supports the calculation of force fields using both force and structural information from a reference all-atom (AA) simulation.
Additionally, tools are provided for determining transferable force fields from an extended ensemble of AA systems, and for determining and simulating with a pressure correction that allows CG models to reproduce the density and compressibility of the reference AA model.

Dependencies:

  • gcc/g++ >= 4.9.2 OR icc/icpc >= 13.1
  • CMake >= 3.0
  • OpenMPI >= 1.9.1
  • A linear algebra library, such as LAPACK/BLAS or Intel MKL

Building and Installation

BOCS is a loosely coupled set of tools for working with coarse-grained models of molecular systems. The components of BOCS, force-matching and pressure-matching, are each compiled separately. Furthermore, to run pressure-matched models, you will need to utilize the USER-BOCS package that is distributed with the official LAMMPS distribution. Installation instructions can be found in the User Manual in the /docs folder. Briefly, the force-matching and pressure-matching components both utilize CMake. The force-matching component NO LONGER relies on an existing GROMACS installation.