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Some stuff to add to the next version. #131

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mrshirts opened this issue Sep 2, 2024 · 2 comments
Open

Some stuff to add to the next version. #131

mrshirts opened this issue Sep 2, 2024 · 2 comments

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@mrshirts
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mrshirts commented Sep 2, 2024

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
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Some of these are more reviews of enhanced sampling, so many of these won't fit.

@fjclark
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fjclark commented Dec 13, 2024

Which of these do you think should be included?

Do others have opinions?

Thanks.

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