From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Oct 20 2020 - 23:33:22 CDT
If I recall correctly, for Eq. 7, the first three terms all are actually calculated with similar integrals as Eq. 13, noting that u_o and u_a give three and two integrals over PMFs, respectively. The fourth term is the separation, the fifth term is handled analytically, and the sixth term is again similar to Eq. 13.
See the SI of this paper for a more detailed breakdown: https://pubs.acs.org/doi/abs/10.1021/ct3008099 <https://pubs.acs.org/doi/abs/10.1021/ct3008099>
In particular, calculation of the separation term is explicitly shown.
Best,
JC
> On Oct 20, 2020, at 10:14 PM, Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:
>
> Hello,
>
> I am following the tutorial mentioned above (http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf <http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf>) using the geometrical route. I am asking if the last term from equation 7, related to the unbound state conformation, is also reduced to equation 13 (i.e. am I supposed to be using equation 13 to do the computation). My unsureness stems from the fact that the other terms from equation 7 that get reduced to equation 13 have a different form than the last term, mostly the dirac delta function.
>
> Thank you,
>
> Ethan Croitoru
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