From: Sebastian Stolzenberg (ss629_at_cornell.edu)
Date: Tue Sep 02 2014 - 15:12:17 CDT
Dear All,
I stumbled over the following consistency check to see, whether I fully
understand the size-dependent charge correction derived in
Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100,
1206–1215,
for FEP/TI with Ewald summation;
this correction I denote here as cr=0.5*ξ*(q1^2-q0^2), where q0 and q1
are the total charges of the simulated system in the reference and
target state, respectively, ξ=−2.837/L, and L is the length of the cubic
simulation box.
Given:
- cubic water box with length L=67A (or 128A) with 0.15mM NaCl, neutral
net charge
- standard CHARMM36 ff, NPT, PME, NAMD 2.9
FEP experiment 1:
annihilate an Na ion, and let appear a water molecule
(the Na and OH2 atoms are harmonically restrained to the same {x y z}
position)
=> q0=0, q1=-1
=> cr<0
FEP experiment 2:
prior to FEP, delete a CL ion in the box, then
annihilate an Na ion, and let appear a water molecule
(the Na and OH2 atoms are harmonically restrained to the same {x y z}
position
=> q0=+1, q1=0
=> cr>0
I understand that the corrected free energy difference DG_cr is obtained
from the computed DG (e.g. via NAMD FEP) via:
DG_cr=DG+cr
I am confused because in my FEP simulations, DG is nearly identical for
both FEP experiments stated above (to the second digit). Therefore, I
would receive different values of DG_cr for the same alchemical
transformation (Na to water).
Is there something I missed along the lines?
With Thanks and Best Regards,
Sebastian
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