Justin MacCallum

Sure, I get the approximation. I’m just wondering if the absence of these couplings from the Jacobian, combined with the otherwise cyclic / highly coupled nature of this particular system,...

It seems that gromacs also has some [problems](https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.1c03665) with this specific topology. I understand that the cholesterol parameters for Martini 3 are under development and having more stable constraints is...

I played around with adding two dummy angles to specify the missing components of the Jacobian. Cholesterol is approximately planar, so these angles are well defined. I just set the...

Regarding planarity, I just meant that this topology has impropers that keep the "diamond" of constrained atoms relatively planar. This allows me to infer what the missing angles is and...

To add some follow up. In our martini parser, I added code that creates an additional "dummy" dihedral with zero force constant for the special case of cholesterol. The resulting...

Here's a minimal test case for one of the failing systems with dummy angles added as described above. ```python from turtle import pos import openmm as mm import openmm.unit as...

I was afraid you were going to say that... Ideally, we would like to be able to reproduce the energies and forces exactly without modification of the topology. And to...

> Updating the atoms involved in a bond is particularly complicated. At the start of a simulation, it splits up the atoms into molecules based on bonds. If you allow...

I decided to implement this for the Reference platform first, but I'm getting a bit stuck. Let's say my custom force wants to define a parameter `foo`. - How do...

I am having some problems with this. I am using doom emacs with a pretty much vanilla configuration. I have `org-download-method` set to `attach`, as I prefer using org's attachment...