Andrea Rizzi

Hi @Eli-VDB . If I understand correctly, the polymer will play the role of the receptor, not the solvent (which is vacuum) so you can leave `solvent_dsl` out of the...

1. Yes, that sounds correct to me. 2. YANK should save in the experiment folder the state of the simulation right before it NaNned. It might help debugging what is...

Hi @bingxie4 . The problem with mixing replicas is here: https://github.com/choderalab/yank/blob/master/Yank/multistate/replicaexchange.py#L281 . To decide how many Gibbs sampling steps to take when mixing replicas, we're using a heuristic that scales...

We could in principle migrate the fire minimizer to `openmmtools` in a separate PR than the samplers if we need to deploy it there soon. Feel free to discuss the...

Hi @Byun-jinyoung . It looks a YAML error to me. From a brief look, I think it's due to the missing `leap:` keyword in `Ca2` `Mg1` `Mg2` sections, which resulted...

Yes, it looks like another YAML error, but from the YANK parser this time. Could you post the new YAML `molecules` section?

> 100 ligands sets to its target using all 10 GPU performance in the future? Hi Jiyuan. Yes, the bug we're working on should not prevent you to parallelize YANK...

Hi @sawstory . Yes, the pdb file needs to contain exclusively the protein. The ligand must be in a separate mol2 file. From the error you posted, it looks like...

Since the NaN occurs at the first iteration, it makes me think that either the initial structure you feed to YANK has clashes and the minimization was not successful. If...

Hi @tantrev . You are right. Currently, the YAML interface doesn't support fitting torsions or passing the charge density as an input to antechamber so you can't use it to...