Sophia is an educational molecular simulation package. It runs as a plugin to Chimera, a molecular modeling application developed at UCSF. To run molecular simulations, Sophia uses the Molecular Modeling Toolkit (MMTK), which is embedded as a library in Chimera. ChimeraX, the next generation of Chimera, is not currently supported.
Sophia was developed on and optimized for MacOS. It’s still possible to run Sophia on Windows or Linux, but some features will not be available, like Monte Carlo and Langevin Dynamics.
OpenMM is a toolkit for molecular simulation using high performance GPU code.
This is a patch release. It contains a small number of bug fixes, as well as changes to enable two significant additions to the supported platforms.
First, this release provides preliminary support for ARM based Macs. The support has not been extensively tested and should be treated as beta quality. Please try it out and let us know if you encounter any bugs while using it.
Second, we are now providing conda packages for use with Pypy. This is an alternate Python interpreter that uses just-in-time compilation to provide much faster execution than CPython. You can create a conda environment that uses Pypy with the command
conda create -c conda-forge --name pypy pypy
You can find the code, manual, release notes, installation instructions and test suite at the links below.
Documentation: http://manual.gromacs.org/2021/index.html. (includes install guide, user guide, reference manual, and release notes)
New and updated forcefields:
- FF19SB for proteins
- Amber-Dyes parameters for fluorescent dyes and linkers
- SIRAH model for coarse-grained simulations
- Amoeba and GEM polarizable force fields, via gem.pmemd
Now builds with cmake; conversion to python3
AmberTools consists of several independently developed packages that work well by themselves, and with Amber20 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL)