From: David Huggins (djh210_at_cam.ac.uk)
Date: Wed Sep 18 2013 - 05:02:52 CDT
I am using an FEP protocol to create/annihilate an ion in explicit
water with PME electrostatics. From reading, my understanding is that
NAMD uses a uniform, neutralizing charge density to avoid numerical
problems with a charged periodic cell and that this requires a
correction to the energies. Previous posts also suggest that these
energies may be less accurate.
My question is whether this correction term is automatically applied
to the energies that come out of the simulation and out of the FEP
calculations? Is the correction term applied separately to each step
of the FEP calculation, which will have a different charge?
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