Re: NAMD QM/MM alchemical free energy change capabilities?

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Nov 27 2018 - 08:26:34 CST

Hi Braden,

Unfortunately I don't believe any of the features you are requesting are
currently implemented.

1) The alchemical code paths are currently only implemented for fixed
charge and Drude MM force fields.

2) You *might* be able to set up an ABF simulation with an explicit
interface for this purpose. This has more commonly (only ever?) been done
for water/alkane and water/lipid interfaces. If you are ok with relative
solvation free energies, this is probably the recommended route.

3) The QM and QM/MM interactions in NAMD are taken directly from the QM
software -- my understanding is that PME is only applied to the MM
interactions unless the QM engine also supports PME. QM/MM w/PME is a much
more advanced feature than most people seem to give it credit for and I can
only think of three or four programs (all semiempirical) that have actually
implemented it (and probably all differently). For QM regions with neutral
charge, not using PME is probably not a disaster.

HTH,
BKR


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