Dear Amber Community,
We excited to communicate a number of new methods and important advances
in AMBER's alchemical free energy capability. These include:
1. robust softcore potentials that form part of a new framework for the
design of optimized alchemical transformation pathways:
https://pubs.acs.org/doi/full/10.1021/acs.jctc.2c00725
2. alchemically enhanced sampling (ACES) method for increased
precision: https://doi.org/10.1021/acs.jctc.2c00697
<
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1021%2Facs.jctc.2c00697&data=05%7C01%7Cyork%40chem.rutgers.edu%7C1449d96571c94d9ea90f08daedc5eed5%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638083731952150631%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=NOvdDXjqOftYApqvfhoZt3NjWWd3fHo5D9YxEWgwtNU%3D&reserved=0>
3. first-generation automated workflow for production free-energy
simulation setup and analysis (ProFESSA):
https://pubs.acs.org/doi/full/10.1021/acs.jcim.2c00879
Updated links to related papers can be found here:
https://theory.rutgers.edu/publications.php?title=free+energy
We are now working to put together some useful updated tutorials for how
the new methods can be used - and I will provide updates as they become
available. We would greatly appreciate constructive comments and
discussion from all of you using these tools to solve problems in the field!
Related to this - *we also have a new open Postdoctoral position**at the
LBSR* to work on cutting-edge of development of next-generation
alchemical free energy methods and quantum/machine learning force fields
for drug discovery:
https://jobs.rutgers.edu/postings/188231
Scientists with interest/experience with free energy simulation methods,
machine-learning potentials, or GPU programming encouraged to apply!
Best wishes to all in the New Year!
Darrin York
--
======================================================================
Darrin M. York : Distinguished Professor
: Henry Rutgers University Chair
Institute for Quantitative :
Biomedicine and Department of : Director, Laboratory for
Chemistry & Chemical Biology : Biomolecular Simulation Research
:
Rutgers, the State University :Darrin.York.rutgers.edu
of New Jersey : fax: +1-732-445-4320
174 Frelinghuysen Road : phone: +1-848-445-5199
Piscataway, NJ 08854 USA :http://theory.rutgers.edu
======================================================================
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Received on Mon Jan 16 2023 - 09:30:02 PST
