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This issue tracks all the relevant tasks needed for the release of SMORES v1.0.0 and provides the context necessary for achieving this. This post is a living doc and will be kept-up-to-date as develop…
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I've been running hamiltonian repex (for relative free energy calculations) using openmmtools. In the openmmtools implementation, we first propagate all replicas (run MD) and then compute the energy o…
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This is related to #3166 where I am trying to write a class that creates an alchemical hybrid system for running relative free energy calculations. The hybrid system will handle:
1) alchemical modif…
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### Description
I am attempting a prediction of the enolase dimer with its ligand 2PG by running these commands:
```
$ mkdir data
$ wget -O "data/2PG.sdf" "https://files.rcsb.org/ligands/downl…
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We need the ability to create OpenMM `System` objects with context parameters that allow us to perform relative free energy calculations between two `System` endpoints.
We presume that the user start…
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May I know if I can specify multiple GPUs in a single run? If so, could you please let me know the command?
Thank you so much,
Junjie
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To clarify, I used the command line [Sterimol](https://github.com/bobbypaton/Sterimol), but the algorithm it uses looks the same as wSterimol.
I was getting values for CHF2 and CHCl2 that seemed t…
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Brainstorming things to do before we can start using this code more reliably.
Tagging @jchodera @gregoryross, feel free to add points by editing (assuming you can) or replying.
- [x] Clean up the r…
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Hey guys,
I was recommended to post this issue here by @jchodera.
I've been trying to use openmmtools' alchemy.py code to compute solvation free energies of an ethanol molecule in water. The mai…
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Hello,
I am trying to perform alchemy using the charmm36 forcefield but I've noticed that there are remaining forces when lambda is set to 0. In the LysozymeImplicit test system for example, the px…