[AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18

From: Braden Kelly <bkelly08.uoguelph.ca>
Date: Tue, 27 Nov 2018 08:10:01 +0000

Hello,


Amber documentation covers Free Energy calculations, such as thermodynamic integration and using other methods such as BAR. It independently discusses QM/MM as well. However free energy calculations, specifically alchemical changes in which a molecule is decoupled from the system, or mutated into another molecule, using a lambda parameter that changes from 0 to 1 or vice versa, are not discussed in the context of QM/MM.


There is a post in the mail list from 2010 regarding TI when using QM/MM. There was an issue, but the issue wasn't that TI couldn't be done in QM/MM. This has me hopeful.


Can free energy methods such as TI, BAR, etc. be performed in a QM/MM simulation in amber 18?


I am specifically interested in hydration free energies of small (<50 atoms) organic molecules.


Thanks,



Braden Kelly

PhD. Candidate, E.I.T

University of Guelph

Biophysics Interdisciplinary Group (BIG)

"I feel more like I do now than I did when I first got here."


[1495766834308_mini_wolf_noir.jpg]





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Received on Tue Nov 27 2018 - 00:30:02 PST
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