Dear all,
It is my pleasure to inform that a new tutorial about how we can perform constant pH and Redox Potential MD (C(pH,E)MD) using Amber is now available at: http://ambermd.org/tutorials/advanced/tutorial33/index.htm
This methodology allows the theoretical study of electrochemistry processes, including when pH effects also play a role. It has been introduced in Amber18 and is available both in sander and pmemd. The procedure to prepare input files, run the simulations, and analyze the results when running with a constant redox potential is similar to what is done in constant pH simulations. Predictions of midpoint reduction potentials can be obtained with the same easiness as pKa predictions in CpHMD. Amber18 also supports Replica Exchange MD simulations along the redox potential dimension (E-REMD), which provides a better convergence efficiency. More information about the C(pH,E)MD and E-REMD methodologies and their implementation into Amber can be found at this recent publication by the Roitberg group: https://doi.org/10.1063/1.5027379
Should you need any further information, please do not hesitate to contact us.
Best regards,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
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Received on Sat Sep 01 2018 - 06:00:02 PDT
