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Hi `alchemlyb` developers,
Thank you all for the development of this package. I was using `alchemlyb` to analyze some output files from the simulation performed by GROMACS. When using the function `e…
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@jchodera I was trying to run hydration free energy calculation of phenol. I would like to input Yank by using openmm files of the serialized systems (vacuum and solvated phases). I made a .yaml scrip…
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Hi there
I am trying to upload my own countmatrix and sample metadata table using the interactive version of the tool, but it doesn't seem to be reading my input tables correctly. I made my tables …
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During the rerun step, `gmx mdrun -rerun` is used to obtain potential energies of each of the sampled conformations of the system using every hamiltonian. During this process, if the potential energy …
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Virtual sites are atoms the coordinates of which are built frame by frame from the coordinates of other atoms. MDAnalysis reads the coordinates of these atoms as for any other ones. Yet, it does not r…
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JOSS Review: https://github.com/openjournals/joss-reviews/issues/6970
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Hi I looked through you submission. In ge…
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Some businesses require/mandate that the virtual tracks must be present in the CPL in a specific order. Currently this is not really possible or obvious (initially the order of presence in the deliver…
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Related to #114. Currently, I store the `Bond`, `Angle` and `Dihedral` parameters based on `atom_indices`. It might be nice to be able to support the `PotentialKey` type to be a tuple of atom indices.
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## Part of JOSS review : https://github.com/openjournals/joss-reviews/issues/6970
Dear developers,
Do not know how much of additional work it can be. I was thinking would it be feasible to add s…
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Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS …