Alexander Matthew Payne
Alexander Matthew Payne
I'm back for another problem related to #3152 :) So this is a problem caused by a disagreement about how to label terminal caps. From the [CHARMM-GUI FAQ](https://charmm-gui.org/?doc=faq) > Some...
Originally identified in #164 but I didn't realize what the problem was at the time. This didn't occur in openmm7.4.2 but does in the current available version of openmm7.5. I...
I have state A and state B structures, and I am running metadynamics with RMSDForce with the RMSD from state A to state B as my collective variable. Doubts about...
I know this was not put in the original manuscript because it wasn't ready at the time but I think pretty soon we should consider adding it!
"SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome." https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab977/6425545 This came up about a month ago but no one has made an...
## Description I have been working on starting a repo to collate some attempts at building a homology model of nsp13 bound to ATP / RNA to do CADD. ##...
Several times now I have been looking for something I know is on the website but just can't seem to find it - for instance, I just wanted to download...
**Not a bug, I just didn't see a format that looked right** There are a WHOLE bunch of 3CLpro (Mpro, Main Protease, nsp5) structures. And potentially a WHOLE BUNCH of...
As it says on the label... validation.py should populate classes such as "ValidProteins" dynamically from the data/proteins directory files, so that users can simply add the yml files instead of...
Since significant chunks of the code (~thousands of lines) in this repo are copy-pasted from https://github.com/choderalab/perses (and some bits from https://github.com/choderalab/openmmtools), which constitutes a ton of hard work from graduate...