[gmx-users] about estiminating the binding free energy by LIE method

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Thu Apr 30 08:05:28 CEST 2009

Dear All:

         I would like to estimate the binding free energy between a  
drug molecule and its receptor. Inorder to do this, i run a MD  
simulation in which PME method was used to deal with long range  
electrostatic interaction.
I need to calculate the VDW interaction energy and electorstatic  
interaction energy between the drug and its enviornment to calculate  
the free energy(I cannot use the g_lie tool since I know I have to  
mind the PME contribution).

          For VDW interaction energy, i calculate the  
LJ-SR(drug-enviornment) and LJ-LR(drug-enviorment), so the VDW  
interaction energy is the sum of them.However, I got PROBLEM when i  
try to calculte the electrostatic interaction energy:  if i use  
g_energy to read energy form .edr file, there is onley Coul-SR, but I  
also need the Coul_LR to calculate the electrostatic interaction  
energy.By checking the previous questiones and answers, I know that  
Coul.-recip.is the contirbution of PME. But, the "Coul.-recip" read  
form .edr file by g_energy is not the long range electrostatic  
interaction energy between the drug and enviorment, it seems to  
contain other thing. How can i get the long range electorstatic  
interaction between the drug and the enviornment?
          Does any one can be so kind to give me some advise? Thank  
you very much.

                                Best Regards
     R-X Gu

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