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.
- 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
- libtirpc >= 1.1.4 (required for XDR support via 'xdr.h')
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.
BOCS v5 is a major update to the overall code and implements a variety of features. In particular it implements local density, square gradient, and external potentials into the force-matching equations.
New tools introduced include:
ldcalc - calculates local densities and gradients of local densities for a given w(r) selected by the user (5 options available)
LDPDF - calculates sampled distributions for local density and square magnitude of the local density gradients for each particle
These potentials can be simulated using a modified version of PKG-BOCS, which is currently distributed in the lammps/lammps:develop branch and will be included in future releases. We have included documentation for PKG-BOCS along with examples in the official LAMMPS distribution.
v5 also includes new tutorials/documentation :
- for using Doxygen to generate BOCS documents
- fast examples and README for key BOCS files: *.btp, par.txt, map.*.top [force-matching], config.ini [pressure-matching]
- for simulating and recovering External field potentials
- for constructing and simulating LD potentials.
- for interpretting cgff output
This version also makes the faster algorith default. [Skip_Triple_Loop] is now defunct, this is the default behavior. If desired [Use_Old_Algorithm] can be used to call the triple loop.
More details are available in the 2nd release manuscript (Lesniewski, DeLyser, Noid "Progress toward a better BOCS: systematic coarse-grainiong with local density potentials" (2026)) which validates the implementation and distributes data/test cases.
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.
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.