Finlay Clark
Finlay Clark
Hello, Recent changes to ipywidgets have [broken NGLView](https://github.com/nglviewer/nglview/issues/1032) - ensuring version
Hello, I'm running BSS version 2022.1.0, 8.g3f6b1c18 on linux, installed using conda. I'm attempting to run a short simulation with the gromacs input files supplied [here](https://github.com/bayer-science-for-a-better-life/abfe-benchmark). All relevant inputs/ notebooks...
Hello, I'm running ABFE calculations using a version of Sire modified to use Boresch protein-ligand restraints (https://github.com/fjclark/Sire/tree/feature_boresch_restraints). Previously, I have had no issues with the LJ correction, but now I...
Hello, When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free...
**Describe the bug** I've recently been trying to implement multiple distance restraints for absolute binding free energy calculations in BioSimSpace and SOMD ([modified BSS](https://github.com/fjclark/biosimspace-openbiosim/tree/feature_mdr), [modified sire](https://github.com/fjclark/sire-openbiosim/tree/feature_permanent_mdr), and an [example of...
This PR addresses https://github.com/alchemistry/alchemical-best-practices/issues/129 by adding a short discussion of newer ABFE restraints. I've also added a sentence with references to methods for automated Boresch restraint selection. Thanks.
It might be helpful to discuss newer ABFE restraint schemes such as those proposed [here](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791) and used in [this workflow](https://www.nature.com/articles/s41596-021-00676-1), and the "distance-from-bound-configuration" restraints proposed [here](https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00447) and used in [this...
My understanding is: subsampling is recommended so that Equation 4.2 of [Kong et al., 2003](https://academic.oup.com/jrsssb/article/65/3/585/7110677) , which is derived for uncorrelated samples, can be used to estimate the variance. However,...
# Proposed Change Expand discussion of uncertainty estimation and move sections to the second paper as appropriate (e.g. cycle closure). # Proposed Authors and Reviewers Please confirm (before the end...
# Proposed Change Make Figure 1 the "central axis" of the paper. Possibly update/ create new full-page figure and expand so that it shows a “dummy workflow” for an alchemical...