[gmx-users] estimate free energy bu LIE method, about long range electrostatic interaction

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Thu Apr 30 08:16:22 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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