Noah
Noah
Hi Cédric, me again. Am I right in understanding that these index numbers relate to the prolif.Residue atom indexing? Do you have any suggestions for how to access the index...
Haven't figured out how to extract information like bond angle or distances from the prolif/interactions/Interactions class but you can pull this information from the fingerprint dataframe. ``` from rdkit import...
Something I noticed when trying to create prolif molecules is that the rdkit mol user assigned property 'map index' was missing if I used mp.Pool. I imagine this is the...
Just to come back to this - It seems like the solution I posted above has its issues. If I try to access map index property on a mol run...
How to warm up a system followed by NVT/NPT equilibration while slowly removing backbone constraints
Thanks for the reply @peastman I also just wanted to check that it's normal behaviour for my protein to be positioned outside of the solvent box when viewing the trajectory...
How to warm up a system followed by NVT/NPT equilibration while slowly removing backbone constraints
Okay great thank you Peter. Last question (Hopefully) - If I'm using a Langevin integrator (and no barostat) does that mean I'm running an NVT simulation? My understanding is yes,...
How to warm up a system followed by NVT/NPT equilibration while slowly removing backbone constraints
Is it possible to remove a barostat from a system once having run an NPT simulation?
How to warm up a system followed by NVT/NPT equilibration while slowly removing backbone constraints
Yup you're right - I appear to have modified my code to account for this but hadn't posted on this thread.
An application where this might be useful would be multitemperature PDBs
Hi Esther, Sorry for my slow reply too. Thanks for updating. Absolutely will try with the new yaml file and let you know!