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We should check the error induced in computed binding free energies by using `CutoffNonPeriodic` with various cutoff radii.
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In the case of starting vba with the correct parameters, I expect it to evaluate the model twice to compute two free energies, which will be close enough for the algorithm to stop.
In our current i…
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It would be useful to have a lightweight package for easily reading, interrogating, manipulating, and doing analysis of the JSON analysis files we generate from fah-xchem. To do this, we currently nee…
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I'm trying to debug an odd issue in the newest [Folding@home Sprint 5 dashboard](https://fah-public-data-covid19-moonshot-sprints.s3.us-east-2.amazonaws.com/dashboards/sprint-5/sprint-5-x12073-monomer…
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[Kollman, Peter A., Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, et al. “Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Me…
cramg updated
3 years ago
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For the latest development code I get:
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* MPI error 672736783 in mpi_cart_sub @ mp_cart_sub : Other MPI …
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Dear openmmtools team,
I am trying to calculate the hydration free energy of pyrene molecule in a water/DMSO mixture and obtain nonphysical results.
Here is a brief description of what was done:…
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The attached example crashes when the trying to use PTR in residue #6 on the ligand because there are no rotamers for PTR, even though we want to use the WT rotamer.
The field that is causing the …
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It would be useful if we could refactor [`stats.py`](https://github.com/OpenFreeEnergy/cinnabar/blob/main/cinnabar/stats.py) into a class API so that we could drop in different solvers.
Right now, …
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When I tried the script to convert pdbqt to pdbs without any options it converted pdbqt.vina into individual pdb files. The following are the individual pdb files with binding free energies.
Gen_1_…