Lester Hedges

Thanks, I'll give that a go. > The only thing I would worry about is whether negative numbers are disallowed for various parsers - thinking of PDB or AmberPrm here......

This works. I'll test further to see if it causes issues with other parsers, etc.

Hi there, This is a question that can only fully be answered using knowledge about the system you intend to simulate. For our purposes, we are primarily interested in binding...

Closing since this is a general QM/MM question, rather than a Sire issue.

Hi @Roy-Haolin-Du. Are you able to share a `somd` working directory so that I can debug locally? I tried adding some restraints to a local test file that I use,...

> Does this mean that atom 38387 is being restrained to the position of atom 454? No, the dictionary keys specify the indices of additional dummy atoms that are harmonically...

The functionality was intended to be combined with the `addanchors.py` file contained in [this](https://github.com/user-attachments/files/21120122/somd1_restraints.tar.gz) archive. Apparently @jmichel80 wrote the code and @mb2055 pushed it, so it's probably worth chatting with...

I can only assume that the required code (what was in the PR linked to above) was never added to the PME version of SOMD.

No problem. From what I recall this was a prototype implementation intended to be tested by industrial collaborators, hence why it not fully featured. It probably wasn't intended to be...

Hi Roy, I'm not of the best approach. This isn't something that I've tried before. I'd suggest using the `extra_options` keyword argument to overload the default values and see if...