As per my previous note that aMD log energies do not correspond to the
mdcrd coordinates, I am trying to recompute the aMD boost based on output
from imin = 5 (apparently iamd > 0 is not valid with sander when not
running MD).
In any event, I tried re-doing the calculations in amdlog "by hand" and am
having some trouble. The dihedral boost energies are matching up perfectly,
with differences of <10^-9. However, the total potential boost energies are
nearly always off by ~0.1 kcal/mol. By manually fiddling with the input
potential energy, I could see in a few examples that adding ~1.5 kcal/mol
caused the error to mostly disappear.
At first I thought that maybe some of the more exotic CHARMM force field
terms were being omitted (I'm using a chamber prmtop), but now I'm pretty
sure it's because the boost for the total potential energy is being
computed with the dihedral boost energy included. This was not the behavior
I expected given the nature of the amdlog output; is this intentional? I'm
not really sure this will affect simulations all that much, but I thought
I'd bring it up anyway.
Cheers,
Brian
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Fri Apr 03 2015 - 13:00:02 PDT
