**From:** JC Gumbart (*gumbart_at_physics.gatech.edu*)

**Date:** Tue Oct 20 2020 - 23:33:22 CDT

**Next message:**zeynab hosseini: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."**Previous message:**Abhijit Gogoi: "Velocity MAP calculation in VMD"**In reply to:**Ethan Croitoru: "Protein:ligand standard binding free energies clarification question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
*

**Next message:**zeynab hosseini: "Re: well-tempered metadynamics deforms the water box and the system becomes unstable.."**Previous message:**Abhijit Gogoi: "Velocity MAP calculation in VMD"**In reply to:**Ethan Croitoru: "Protein:ligand standard binding free energies clarification question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Thu Dec 31 2020 - 23:17:14 CST
*