[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation
devawatidutta at gmail.com
Wed Jan 5 07:06:36 CET 2011
I am using Gromacs 3.3.2 version for molecular dynamics
simulation of my protein-ligand complex. I want to calculate the free energy
of binding through LIE method. While extracting the LJ and coulombic energy
values using g_energy command,there are many options like LJ-14, LJ-SR,
LJ-LR, Coul-14, Coul-SR, Coul-recip etc. I am unable to decide which values
should I use for free energy calculation .Which of the following options
should I consider.
1. Should I use only LJ-SR and coul-SR?
2. Should I use the total energy values i.e LJ-SR+LJ-LR?
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