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I propose that we add a new FEP (free energy perturbation) module, as `dc.fep`.
Introduction
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Free energy perturbation has become an increasingly powerful technique in modern drug di…
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Using command line args it should be possible to pass accelerator suffixes to all pair styles without having to modify the input scripts themselves. This seems to work corretly for the pace pair style…
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I'm just collecting some ideas to consider after the 1.0 release.
## Overall optimization
- [ ] Optimize code based on profiling
- [ ] Non-cubic/rectangular boxes (truncated octahedron, dodecahe…
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It probably should be; it's supported in the biggest simulation engines, has valid scientific basis, and sees use in force fields elsewhere.
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We should look into why calculations spend so much time writing sampler states, and why this time increases with iteration number.
Some thoughts:
* We very likely should not be calling `sync()` ev…
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Hello,
When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free energies …
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I think this a really crucial point since it touches on the very core purpose of our app and also concerns all views/areas of the app.
1. There needs to be more differentiation for public transport…
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Currently we have a mismatch where we have some details about how solvation happens in the SolvationSettings and some in SolventComponent.
My proposal is that **anything that defines the molecular …
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If we want to report support for AMBER FEP in this tutorial we will need to merge in devel the functionality currently in https://github.com/michellab/BioSimSpace/tree/feature-amber-fep
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reported by: @CloudyLex
The appendix to this paper has a nice discussion of Rayleigh scattering. We could use this to improve our treatment.
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A New Generation of Los Alamos Opacity Tables
Col…