[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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