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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.

Important Change for BOCS3

BOCS v3 implements a new (faster) algorithm for calculating the G matrix. However, the default behavior is still to use the original algorithm. To use the new algorithm, simply include [Skip_Triple_Loop] in your par.txt file. See the new manual for more information.

BOCS v4

BOCS v4 slightly modified the format of .btp files. Any .btp file created with an earlier version of BOCS will cause errors with the newer BOCS format. If you try to use an old .btp file with a newer version of BOCS, BOCS will print a message saying that you need to re-translate the dumped .tpr file with the new version of BOCS.

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Bottom-up Open-source Coarse-graining Software

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