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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 30 09:20:26 CEST 2009

mircial at sjtu.edu.cn wrote:
> 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?

True, Coul.-recip has other components in there. There's no way to
decompose it. However the quantity in which you are actually interested
is the difference between the long-range electrostatic interaction
energy of two states, which in the limit of infinite sampling converges
to the difference between Coul.-recip values. Presumably this issue has
been dealt with in the literature, so look for recent published
methodologies using the LIE method.


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