[AMBER] GPU-accelerated thermodynamic integration available in Amber

From: Darrin York <york.chem.rutgers.edu>
Date: Tue, 12 Sep 2017 09:01:40 -0400

Hi all,

We wanted to give everyone an update regarding our GPU-accelerated free
energy methods in Amber, and in particular, our implementation of
thermodynamic integration <http://theory.rutgers.edu/?q=node/288>
reported very recently in JCTC
(http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00102). The code
typically delivers over 2 orders of magnitude of speed-up relative to a
single CPU core for the calculation of ligand–protein binding affinities
with no statistically significant numerical differences and thus
provides a powerful new tool for drug discovery applications.

The code (pmemdGTI) is ready for beta release as a patch to Amber 16,
and is available as through the Laboratory for Biomolecular Simulation
Research <http://lbsr.rutgers.edu/>, a new core laboratory at Rutgers
dedicated to the development and application of innovative biomolecular
simulation tools, on the download page:
http://lbsr.rutgers.edu/software-downloads

Also available are new tools for free energy analysis such as the the
vFEP method <http://theory.rutgers.edu/?q=node/106> for robust
determination of free energy profiles.

We hope you find it useful, and look forward to getting your feedback,
discussion, and suggestions for further extension and next sets of features.

cheers!

Darrin 

-- 
--
======================================================================
Darrin M. York                    : Henry Rutgers University Professor
                                   : Director, Cyberlearning
Center for Integrative Proteomics :    Innovation & Research Center
    Research 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 Tue Sep 12 2017 - 06:30:04 PDT
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