Lester Hedges
Lester Hedges
As reported by @msuruzhon, pickling/unpickling large BioSimSpace objects has very poor performance on macOS. Using [System.pickle.tar.gz](https://github.com/michellab/BioSimSpace/files/9103247/System.pickle.tar.gz) we see: ```python import BioSimSpace.Sandpit.Exscientia as BSS import pickle import time a = time.time()...
This is a thread to discuss the creation of a tutorial showing how to implement steered molecular dynamics in BioSimSpace.
This issue thread is used to discuss support for parameterisation using force fields from the [Open Force Field Initiative](https://openforcefield.org/). Development is underway on the [feature_openff](https://github.com/michellab/BioSimSpace/tree/featuhttps://github.com/openforcefield/openff-toolkitre_openff) branch. An overview of the...
This is a thread to discuss the creation of a tutorial showing how to implement funnel metadynamics within BioSimSpace.
As anticipated, it turns out that the presence of crystal waters are extremely important for obtaining the correct binding mode of certain ligands. BioSimSpace needs to be modified so that...
This is a thread to discuss the creation of a tutorial showing how to implement free-energy perturbation using a network, e.g. generated by LOMAP, within BioSimSpace.
I've made a few minor updates to BioSimSpace such that all dependencies for Sire and BioSimSpace are now available through the `conda-forge` channel (other than the `fkcombu` tool, which we...
This PR fixes the offset used when injecting the inclusion of external `posre*.itp` files into a GROMACS topology. The logic used previously meant that the offset was incorrect, meaning that...
Opening this thread for a discussion about strategies for migrating Sire and BioSimSpace to the [OpenBioSim](https://github.com/OpenBioSim) GitHub organisation. ### Timing Do we want to do this ASAP, or coincide with...
**Describe the bug** Hello there, Many thanks for this excellent program, which has saved me from many hybrid graphics related headaches over the years. I have recently started using a...