Roadmap

Roadmap for Alchemlyb

Aims

(Open for discussion!)

1. To provide a modular, robust, and rigorously tested library for alchemical free energy calculations.
2. To provide state-of-the-art and best-practice implementations of algorithms for (1) pre-processing and (2) estimation
3. To provide modular tools for the analysis of sampling and convergence of alchemical free energy calculations.
4. To make it easy to couple structural analysis (e.g. conformations, dihedrals, other abitrary coordinate-based features, solvation, ligand degrees of freedom) with alchemical analysis. alchemlyb already makes it easy to pre-process "alchemical" dataframes (dH/dl or u_nk timeseries) by slicing but this needs to be shown-off (examples, tutorial).
5. To become a community driven project.

Interested parties

• Oliver Beckstein @orbeckst, Arizona State University
  • currently maintaining the library (in stewardship mode...)
  • uses it in-house
• Michael Shirts, University of Colorado Boulder
  • Working to get the nice features of alchemical-analysis on top of an extensible library.
• Bryce Allen, STX, @brycestx
  • Somewhat limited bandwidth but working with @shuail and @marcelschumann2 to contribute amber parsers and tests.

Immediate/pressing requirements

parsers

• Amber TI #10
• Gromacs extended ensemble #14:
  • lambda exchange

test data

We need small data sets for test driven development. Data sets are packaged separately in the alchemistry/alchemtest package. See contributing data to alchemtest for further details.

• Amber TI #10
• Gromacs extended ensemble #14