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Is there a possibility to make CrystalExplorer perform intermolecular interaction energies calculation by running TONTO in parallel (multi-core) under Windows 10?
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I wanted to know if it is possible to use PyMBAR to generate a 2D Potential of Mean Force (PMF) graph using energies obtained from NAMD. The energies need to be reweighted though as I used accelerated…
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I'm interested in calculating the RMSD between two molecular crystals with the PAC algorithm; however, as I understand the information of the forcefield is required. Otherwise, I get the following er…
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Using the same base objects from the other protocols (`NonEquilibriumCyclingProtocol` and `RelativeHybridTopologyProtocol`) we want to implement a protocol that supports protein mutation based on the …
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(Links below will open the PDF with the Google Docs viewer. Default GitHub behavior would be to download the file instead.)
**Article file diff**, using `latexdiff`
[revised_manuscript_marked_up.…
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Awhile ago I made a biopython issue mentioning a small bug I saw in the DNA nearest neighbor values. I caught that because I was using biopython's DNA nearest neighbor energies to bootstrap a library …
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For the paper #147 it would be very beneficial to demonstrate that GromacsWrapper has been used elsewhere, especially in software or work that can be cited.
Please add to this issue any citation fo…
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This is a thread to discuss the creation of a tutorial showing how to implement free-energy perturbation using a network, e.g. generated by LOMAP, within BioSimSpace.
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I’ve understood that a dense/exact diagonalization method (e.g., LinearAlgebra.jl's `eigen()`) is currently used for diagonalizing projected Hamiltonians during the sweeps (please correct me if I’m wr…
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Right now, the SmallMoleculeProposalEngine does not correctly respect protonation states, due to code that converts the OpenMM topology to an oemol (will raise issue there).