New and improved features¶
Density-guided simulations¶
Users can now apply additional forces from three dimensional reference densities. These forces can be used to “fit” atoms into the densities by increasing the similarity of a simulated density to the reference density.
Multiple protocols are available for how to calculate simulated densities as well as how the similarity between a reference and a simulated density is evaluated.
Virtual site on the line through two atoms at fixed distance¶
This is use useful for e.g. halogens in the CHARMM force field.
gmxapi Python support¶
Data flow driven simulation and analysis from Python. Initial support includes simulation trajectory ensembles, looping, simulation parameter modification, and wrapping for command line tools or custom Python functions.
New modular simulator¶
A new approach for how to combine individual calculation steps during a single simulation step is introduced, with focus on extensibility and modularization. This simulator is the default now for simulations using velocity-verlet in NVE, NVT (v-rescale thermostat only), NPT (v-rescale thermostat and Parrinello-Rahman barostat only), or NPH (Parrinello-Rahman barostat only), with or without free energy perturbation.