-
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…
-
Trying to enumerate all the ways that perses can be used, and might be used in future
-
Hi everyone,
I just finished 2 sets of Gromacs simulation for my system (RNA+ligand). The first set has only ligand (20 runs). The second set has both RNA and ligand (30 runs). Each simulation is ru…
-
Hi there, I noticed that alchemical analysis only uses a single core at a time and doesn't utilize gpus at all. I'm wondering if their is any intent of adding this to the code in the near future?
Gene…
-
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…
-
@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…
-
I see that there are [plans](https://github.com/alchemistry/alchemlyb/wiki/Roadmap#librarify-alchemical-analysis-functionality) to librarify alchemical-analysis with [alchemlyb](https://github.com/alc…
-
**Under construction**
- Is it safe to assume two isomorphic molecules are parametrized identically? **Yes**
- Without this, each i.e. solvent molecule would need its own `[ molecule ]` directiv…
-
Lee-Ping would like to be able to compute arbitrary solvation free energies for a molecule in another type of molecule.
-
Dear Mobley lab,
I am trying to run the alchemical-analysis tool on a set of output files from Amber TI simulations. The tool successfully computes dG, but fails to compute BAR/MBAR results and out…