In CHARMM, patches are generally applied at the modelling stage. If you used a patch while generating your PSF file, it should contain everything it needs to be read correctly.

Every atom in a residue is required to have a unique name. Because your atoms are all named either "H" or "C", it assumes they are alternate locations for the same two atoms rather than different atoms.

No, it does not use tensor cores. We've looked into it, but there isn't really anything they would be useful for. They have a couple of problems. 1. Really all they do is matrix multiplication. They aren't useful for anything that doesn't look like a matrix multiplication. 2. They don't support 32 b...

What do you expect to happen in that time? Is it a stable molecule or a very flexible one? 1 million steps is 4 ns. How much conformational change do you expect it to undergo in that time?

You're better off just using a single GPU. For one thing, 100,000 atoms isn't really that large. It probably doesn't provide enough work to saturate multiple 4090s. For another thing, the performance of multi-GPU simulations depends strongly on the speed of communication between GPUs. All consumer G...

That isn't an architecture we've ever tried to support. You could try to figure out how to compile it. It would definitely require some changes to the build scripts, but you might be able to do it, and it might even work. Then again it might not...

Correct on both.

I think it's just different units. You're printing the units in kcal/mol/nm. If you instead print them in kcal/mol/A they'll be 10 times smaller. That's probably what CHARMM is using.

I already said: all standard integrators apply constraints correctly. That correction is part of RATTLE. Other algorithms account for velocities in other ways, but all of them handle them correctly.

I don't understand your question. It is always applied. It's part of the algorithm.

All the standard integrators apply constraints correctly. They use different algorithms in which constraints come up in different ways, but each algorithm handles them in a correct way.