Thank you Alan, that makes sense! And I see from this thread that setting up HMR simply requires passing -heavyh to pdb2gmx, which is easy enough.
One more question, if you two don’t mind. Is there a tradeoff between speed and accuracy with HMR + update on the GPU vs vsites + update on the CPU? In other words, is there an accuracy benefit to using vsites over HMR? I understand that this may be system-specific, but how do the two methods compare?
Thanks again!
Roman