alchemical-best-practices icon indicating copy to clipboard operation
alchemical-best-practices copied to clipboard

Some stuff to add to the next version.

Open mrshirts opened this issue 5 months ago • 1 comments

I guess I am volunteering to add these (unless in some case other people feel like they know it better).

  • We introduced alchemical metadynamics, allowing one to treat the alchemical variable as a CV (https://arxiv.org/abs/2408.11038). This is hybrid technique, but also motivates understanding the accumulation of biases in alchemical space better.

  • We introduced Replica Exchange of Expanded Ensembles (https://pubs.acs.org/doi/abs/10.1021/acs.jctc.4c00484), which basically interpolates between the two methods. This can be put into the hybrid section. One application is doing multiopology switches (https://arxiv.org/abs/2408.11038), which could enhance the sampling of networks of free energy calculations

  • Ryan Hayes and Jonah Vilsec have been expanding the utility of multi-lambda dynamics. Might be worth addressing a bit more here.

  • I wonder if we should explore UFED at all here (Mark Tuckerman's framework).

mrshirts avatar Sep 02 '24 17:09 mrshirts