Toni Mey
Toni Mey
I believe there is some plan on improving the setup instructions, but I am relatively new to all of this and not really in the know. It seems that the...
Default settings for a 200 ps equilibration simulation with a system of 50k atoms takes more than 24 hours to complete on a typical GPU cluster with an optimised Gromacs...
When loading a molecule form amber prm7 and rst7 and then writing it out to mol2, the atom types are set to dummy, this means the mol2 file cannot be...
It would be nice if sire could support amber style input file for charmm style forcefield formats, containing CMAP corrections, currently amber.cpp throughs an error when reading the attached input...
I am using this issue to help with merging [this](https://github.com/michellab/BioSimSpaceTutorials/tree/main/04_fep) and [this](https://github.com/michellab/bssccpbiosim2022) set of FEP tutorials. I'll keep updating to dos adding questions etc. Questions: - [x] We keep the...
@lohedges, @annamherz @jmichel80 @fjclark @AdeleHardie @dlukauskis, I have created a style guide here: https://github.com/michellab/BioSimSpaceTutorials/blob/main/Style_guide.ipynb Can you look over it and let me know what you think. It would be good...
Posting already but will edit more to fill in details in abit. Text: General readme: - [ ] Make sure it contains all essential information including installation etc. It seems...
Hi, I was wondering if you have any 3D structures available for the dataset, or you only worked with SMILES. Thanks for the help. Best wishes, -Toni
Having this community benchmark means we should also define a set of people who will check that it adheres to the standard as discussed in the accompanying paper. Maybe this...
Data for the plotting and the plotting scrip for Figure 7 is missing. Font should be adjusted to Helvetica.