Open-source GPU accelerated molecular dynamics engine for alchemical free-energy simulations. Built on top of Sire and OpenMM. The code is still under active development and is not yet ready for general use.
First create a conda environment using the provided environment file:
mamba create -f environment.yaml
(We recommend using Miniforge.)
Now install somd2 into the environment:
mamba activate somd2
pip install --editable .
You should now have a somd2 executable in your path. To test, run:
somd2 --help
In order to run an alchemical free-energy simulation you will need to first create a stream file containing the perturbable system of interest. This can be created using BioSimSpace. For example, following the tutorial here. Once the system is created, it can be streamed to file using, e.g.:
import BioSimSpace as BSS
BSS.Stream.save(system, "perturbable_system")You can then run a simulation with:
somd2 perturtbable_system.bss
The help message provides information on all of the supported options, along
with their default values. Options can be specified on the command line, or
using a YAML configuration file, passed with the --config option. Any options
explicity set on the command line will override those set via the config file.
An example perturbable system for a methane to ethanol perturbation in solvent
can be found here.
This is a bzip2 compressed file that will need to be extracted before use.
Simulation output will be written to the directory specified using the
--output-directory parameter. This will contain a number of files, including
Parquet files for the energy trajectories of each λ window. These can be
processed using BioSimSpace as follows:
import BioSimSpace as BSS
pmf1, overlap1 = BSS.FreeEnergy.Relative.analyse("output1")(Here we assume that the output directory is called output1.)
To compute the relative free-energy difference between two legs, e.g. legs 1 and 2, you can use:
pmf2, overlap2 = BSS.FreeEnergy.Relative.analyse("output2")
free_nrg = BSS.FreeEnergy.Relative.difference(pmf1, pmf2)