Iván Pulido
Iván Pulido
We want to be able to deal with protein caps for proteins prepared with the Maestro software or the suite's protein preparation wizard. This will require to check what are...
It should be useful for performing analysis that the `Simulation` object had attributes that helped knowing which ligands or edges are involved. Currently the only way to get this information...
Benchmarking and automated tests for the new FAH generator code from #909 are needed. CC https://github.com/choderalab/perses/pull/909#issuecomment-1046056796
Yes, you are right, we do this in the [examples test](https://github.com/choderalab/perses/blob/main/perses/tests/test_examples.py#L20) in a somewhat dirty way. Maybe we do want to have this yaml file in our package somehow. I...
It would be very useful to have the benchmarks getting run automatically after a new release either on our on premises HPC system or some cloud instance that could handle...
I'm trying to backup some subvolumes in my machine (localhost) to a remote server via ssh. I could manage to create the streams and actually push the first snapshot (0_date_blahblah...
`PeriodicNonequilibriumIntegrator` seems to not be using the `nsteps_eq` parameter to perform any equilibration. Instead, users need to manually call `integrator.step(nsteps_eq)` to run an equilibration before the non-equilibrium part. The signature...
The default behavior for the small molecule pipeline is to reassign velocities when resuming, as shown in https://github.com/choderalab/perses/blob/2ff4a7bb631a93716b64f2bd11dc68a2864402cd/perses/app/setup_relative_calculation.py#L713 Since we now are able to resume velocities correctly, PR https://github.com/choderalab/openmmtools/pull/602 ,...
**Describe the bug** When I tried read a list of molecules form an sdf file and try to apply the `.index` method (`list` method) I get an unexpected behavior. It...