[email protected] 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
