Dan-Burns

Has anybody had any luck getting generating full xml for opc and ions?

I posted an issue ([#642](https://github.com/choderalab/openmmtools/issues/642)) similar to this. I am using openmm 7.7.0 and openmmtools 0.21.5. I also get the same issue with openmm 7.6.0. I have tried to use...

Well, it appears that it was an equilibration issue. I reduced the ReplicaExchangeSampler timestep to 0.01 femtoseconds and also increased the collision rate to 100/ps for a short equilibration, then...

I have to backtrack on my previous comment. I still get the nan error. I am applying lambdas to electrostatics, torsions, and sterics. If I run a LangevinSplittingDynamicsMove where each...

Based on issue [516](https://github.com/choderalab/openmmtools/issues/516) and some of the replex discussion and [scripts](https://github.com/zhang-ivy/perses_protein_mutations/blob/master/code/24_rbd_ace2_repex/resume_repex_parallel.sh) from @zhang-ivy it's clear you have to run it with a hostfile and configfile. You can generate the...

Of course the slurm output makes it look like 4 independent processes started since several print statements are repeated 4 times. These are simulation setup steps though and maybe they're...

Thank you, @zhang-ivy. I assume I can change the line in `exceptions_sterics_energy_expression` from: `'reff_sterics = sigma*((softcore_alpha*(1.0-({0}))^softcore_b + (r/sigma)^softcore_c))^(1/softcore_c);')\ .format(lambda_variable_name)` to: `'reff_sterics = sigma*((softcore_alpha*(1.0)^softcore_b + (r/sigma)^softcore_c))^(1/softcore_c);')` I will see what happens....