Miroslav Suruzhon
Miroslav Suruzhon
As a user that hasn't done much ABFE before I would certainly prefer an explicit parameter, rather than a key in a `property_map` @xiki-tempula .
Sorry for not being very helpful, but I made this system long ago and I don't remember how I generated this, I will update if I recall something. The waters...
Thanks @lohedges I have a couple of comments and I am also going to test it and I will approve once I have tested it on the original system I...
@lohedges I have tested it on a few systems and it seems to work for me. Feel free to merge once you add some tests. Many thanks.
Ah apologies, I should have attached the `itp` as well, this should do it now: [Archive.zip](https://github.com/michellab/BioSimSpace/files/10245964/Archive.zip)
Thanks @lohedges, I think I should be handling the velocities correctly, so I guess that means nothing out of the ordinary is happening, just that the velocities are too big...
Thanks @lohedges I am using the HMR routine from `ParmEd` but the implementation should be the same between both packages. I just tested the `BioSimSpace` function and I get the...
Thanks @jmichel80, strangely `constraint = allbonds` crashes now even at 2 fs, and I am not sure why.
I am using a defensive restrained protocol with OpenMM that runs fine at 4 fs with HMR. However, before running into these issues with SOMD, I pre-minimise the structure in...
Thanks @annamherz and @lohedges I think we might have different issues because with normal hydrogen constraints I get stable simulations at 2 fs and only get instabilities at 4 fs...