Finlay Clark

@xiki-tempula sorry about the slow reply. Does this sound like a reasonable initial approach?: Given that representing the restraints might be more complex than we thought at first, maybe it...

Great. There don't seem to be any issues with interactive nodes with GUI elements - just with NGLView. Cheers

Hi, Thanks for the quick response. Great - I'll update to the latest version. Cheers

The original issue I was having was instability during equilibration using sander through BSS and @jmichel80 mentioned that there had been issues previously with file conversion. To rule this out,...

Thanks very much @lohedges. @jmichel80 will do.

@jmichel80 I can confirm that the AMBER files produced by @lohedges's script work with SOMD. However, test alchemical simulations crash when I use the same config file I'm using for...

I've repeated the calculations, only adding or removing "set_constraints = allbonds" to the config. Adding this consistently causes the simulations to crash during minimisation. I'm running my modified version of...

@lohedges I'm not able to equilibrate the original GROMACS files in BSS using GROMACS - I get failures during my final NPT equilibration. Based on this, it seems likely that...

@jmichel80, it looks like constraints aren't disabled before energy minimisation in runFreeNrg(), only run() https://github.com/michellab/Sire/blob/6ff6b04d56a3b76fb18f7ba2317557d15cd41cb6/wrapper/Tools/OpenMMMD.py#L1686-L1695 . However, even when I modify the my version of Sire to disable constraints before...

Hello @lohedges , As Bayer does not have AMBER, I've been asked to check the consistency between revised input files: [brd4_inputs.tar.gz](https://github.com/michellab/BioSimSpace/files/9819268/brd4_inputs.tar.gz) The AMBER inputs produce stable MD with sander (10...