[gmx-users] estimate the binding free energy. long range electrostatic interaction

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Thu Apr 30 19:34:54 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.
     > Mark
     Dear Mark:

               I read some materials talking about this issue,it is said =20
     that,i should rerun my trajectury
     with the charges of my ligand set to zero, and calculate the =20
     "Coul.-recip" again.Subtract this value from
     the previous "Coul.-recip." and the result is the long range =20
     electrostatic interaction energy between
     the ligand and its enviornment.

               Is this method right?

                                           R-X Gu

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