[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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