The official release of GROMACS 2022 is now available.

• Free-energy kernels are accelerated using SIMD, which make free-energy calculations up to three times as fast when using GPUs
• A new formulation of the soft-cored non-bonded interactions for free-energy calculations allows for a finer control of the alchemical transformation pathways
• New transformation pull coordinate allows arbitrary mathematical transformations of one of more other pull coordinates
• New interface for multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) simulations with the CP2K quantum chemistry package, supporting periodic boundary conditions.
• grompp performance improvements
• Cool quotes music playlist
• Additional features were ported to modular simulator
• Added AMD GPU support with SYCL via hipSYCL
• More GPU offload features supported with SYCL (PME, GPU update).
• Improved parallelization with GPU-accelerated runs using CUDA and extended GPU direct communication to support multi-node simulation using CUDA-aware MPI.

If you are a Spotify user the Cool quotes music playlist may be of interest!

Note:

If you are running on Mac OS X, the best option is gcc. The Apple clang compiler provided by MacPorts will work, but does not support OpenMP, so will probably not provide best performance.

 

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.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2021.tar.gz.

Documentation: http://manual.gromacs.org/2021/index.html. (includes install guide, user guide, reference manual, and release notes)

Test Suite: ftp://ftp.gromacs.org/regressiontests/regressiontests-2021.tar.gz.

 

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

Also

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)