Jochem Nelen

> Yes, it will be slower. Timings are in the gnina paper https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00522-2 I understand not using a GPU will impact the overall docking time by a lot. However, can...

> Presumably you are doing high throughput docking (docking a lot of ligands) in which case running all your gnina jobs on 1 or 2 cores should give you the...

> Modern processors can run more simultaneous threads than they have cores, see https://www.intel.com/content/www/us/en/gaming/resources/hyper-threading.html > > This is only relevant if you have hyperthreading enabled on your cluster nodes. Thanks...

For the Value ctype I picked a regular, single precision float. However we could also use a double precision float if you think this is more appropriate!

> Thanks! Please don't waste too much time on `mypy` issues. It's supposed to be helpful, not annoying. If it becomes too much, we can simply turn it off for...

I added some very basic tests for the prmsdwrapper function. (I basically copied the tests with the rmsdwrapper function and used the prsmdwrapper function instead). I also added a test...

> Thanks @Jnelen! I'm a bit swamped this week too, but I'll try to have a look and reply ASAP. Sorry for the delays. No problem at all. Actually, I...

I'm back from my break! Right before that I actually updated my use-case [(ESSENCE-Dock)](https://github.com/bio-hpc/metascreener/commit/30add4905c776f8d07b7fc0093a6eb3e21c145d1) to work with a time-out and multicore, but I ended up using [Pebble](https://github.com/noxdafox/pebble) since this handles...

Hi, I finally got around to work on a simple benchmark, but I have started to notice quite a notable difference between running the calculations the first time versus subsequent...

Alright, I did some testing, and the performance of the parallel implementation is a lot worse than I thought it would be to be honest.. In the edge-cases tests I...