OpenMSCG

An open-source python package for systematic coarse-graining (including MSCG/force-matching) in computational chemistry and biology. To download OpenMSCG integrated with the mstool backmapping software, visit here: https://software.rcc.uchicago.edu/git/MSCG/mscg-mstool.

Quick Guide

1. Prerequisites

Install a conda package manager/environment: Anaconda or Miniconda.

2. Install package from Anaconda Cloud

conda install -c vothgroup openmscg

4. Test the installation

cginfo

Documentation

See the documentation at https://software.rcc.uchicago.edu/mscg/docs/.

Notes of Updates & Changes

0.7.1

1. Fixed a bug in PBC when an atom is just at the boundary.

0.7.0

1. Add "model_nb3b_bspline" and "model_nb3b_sw" for the NB3B method.

0.6.7

1. Trajectory: add support for scaled coordinates in LAMMPS format.
2. Trajectory: dump type ids in LAMMPS format in CGMAP.
3. Topology: add support of explicit angle/dihedral lists in CGTOP.
4. Add option --exclude for command-line interfaces using pair-lists.
5. Dump alpha/beta logs in Bayesian regression.
6. Update normalization scheme for pair RDFs in CGIB.

0.3.5

1. Enable cross-density for the RLE weighting function in UCG.

0.3.4

1. Allow environment variables OPENMSCG_MAXPAIRS to increase max_pairs in pair-list.
2. Fixed a bug in UCG weight-function for computing local densities.

0.3.3

1. Fixed a bug in CGMAP for incorrect repeat times for sites.

0.3.2

1. Fixed a bug in caching the bspline table.
2. Add the trial version of CLI CGED for EDCG modeling.

0.3.0

1. Release the feature of substracting tabulated forces from the reference trajectories.
2. In CGIB, add screen output for the ranges of the target variables.
3. Distributed workflow of Force-matching assisted by new CLI CGNES.
4. New CLI CGHENM for heterogeneous elastic network modeling.

0.2.2

1. Enable processing of LAMMPS trajectory in that only part of the system atoms are dumped.
2. Fixed bugs in modeling of multiple types of UCG sites.
3. Allow users to setup number of threads for multithreading acceleration.

0.2.1

1. The unit of input values for CGFM angular models is changed from radius to degrees.
2. Add calculation of dihedral angles in CGIB.
3. Add new GaussCut model for the REM method.
4. Change the matrix inversion in CGFM to allow for the singular matrix.
5. Fix a bug in PairList to reduce the need of memory in verlet-list.

0.1.0

1. All basic features are released