[gmx-users] Please rectify free energy problem

pawan raghav pwnrghv at gmail.com
Tue Aug 30 15:52:05 CEST 2011

g_lie calculates the deltaG= alpha(<Vl-s LJ>p - <Vl-s LJ>w) + beta(<Vl-s
el>p - <Vl-s el>w) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either <Vl-s LJ>p or <Vl-s
LJ>w and -Eqq for either <Vl-s el>p  or <Vl-s el>w. My question is when
using only <Vl-s LJ>p for -Elj and Vl-s el>p for  -Eqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?

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