choderalab/openmmtools: 0.13.1 - Bugfix release

In this release: Fix pickling of CompoundThermodynamicState (#284). Add missing term to OBC2 GB alchemical Force (#288). Generalize forcefactories.restrain_atoms() to non-protein receptors (#290). Standardize integrator global variables in ContextCache (#291)

psi4/psi4numpy: v0.3-beta

Psi4NumPy is an interactive quantum chemistry framework for development and education. By leveraging the Psi4 program, integrals and quantities important to quantum chemistry are obtained and then manipulated or contracted using the Numerical Python (NumPy) package. In this way, quantum chemistry can be programmed quickly and concisely while still maintaining a relatively low execution time. A series of short scripts are provided that demonstrate how a user would implement the following methods: Self-Consistent Field (SCF), SCF Response, Moller-Plesset Theory, Coupled-Cluster, Symmetry-Adapted Perturbation Theory, and more. Walkthroughs of quantum chemistry methods detailing both their theory and implementation are shown in order to provide an educational framework for both novice and expert users in the field. Overall, this project aims to remove the gap between theory and implementation. As such, user-submitted scripts and modifications are welcome in order to make a better Psi4NumPy experience for the entire quantum chemistry community. As a note, Psi4NumPy is a constantly evolving framework. Please seek github.com/psi4/psi4numpy for the latest version of the code

openmm/openmm: OpenMM 8.1.0 beta

<p>This release contains many performance improvements, particularly to the CUDA and OpenCL platforms. The largest speedups are for very large systems, in the range of 1 million particles or more, which can now be much faster. Other simulations will also often be faster, though by smaller amounts. Some examples of cases that have been specifically optimized include PME on the OpenCL platform; very small systems (less than 3000 particles) on the CUDA platform; CUDA or OpenCL simulations on Windows; CUDA simulations that are parallelized across multiple GPUs; and CUDA or OpenCL simulations that use CustomHbondForce.</p> <p>This release adds a new class called ATMForce that implements the Alchemical Transfer Method. This is an efficient, relatively easy to use method for doing alchemical free energy calculations. See <a href="https://doi.org/10.1021/acs.jcim.1c01129">https://doi.org/10.1021/acs.jcim.1c01129</a> for more information.</p> <p>There is a new XTCReporter class for writing simulation trajectories to XTC files. This is an alternative to DCD for efficiently storing trajectories. It stores coordinates with reduced precision, which leads to significantly smaller files.</p> <p>When running local energy minimizations, it is now possible to pass a reporter to the minimizer. This allows you to monitor the progress of minimization and optionally to stop it early when custom criteria are met.</p> <p>The GromacsTopFile class now supports GROMACS files that use GROMOS force fields.</p> <p>This release adds a new piece of low level infrastructure for use when writing plugins: the CustomCPPForceImpl class. It is used for writing plugins that are implemented entirely in platform-independent C++. This is useful, for example, when writing plugins that interface to other libraries or programs. By using the new mechanism, the amount of code needed for plugins of that sort is dramatically reduced.</p> <p>One significant feature has been removed: GromacsTopFile can no longer read files that use implicit solvent. GROMACS removed all support for implicit solvent a few years ago, and it had not worked correctly for several years before that. OpenMM continued to support GROMACS files with implicit solvent, but it required you to have an increasingly obsolete version of GROMACS installed on your computer. That support has now been removed.</p&gt

pandegroup/openmm: OpenMM 7.1.1

This is a patch release that includes the following bug fixes: 1731 (Fix substeps division in MTSIntegrator) 1752 (Fixed error adding triclinic solvent boxes) 1756 (Fixed bugs in multipoles with ZOnly axis type) 1757 (Allow docs to build in Sphinx 1.3.1 and 1.5.1) 1761 (Fix bug where CHARMM impropers did not respect toroidal boundary conditions) 1767 (Fixed error with exclusions for Drude particles) 1784 (Fixed bug accessing parameters for CustomHbondForce) 1792 (Bug fixes to CustomHbondForce