[gmx-users] System neutralization in Thermodynamic Integration

Leandro Bortot leandro.obt at gmail.com
Wed Aug 29 22:22:43 CEST 2012

Dear All,

     In order to calculate the binding free energy of a ligand to a protein
I am using Thermodynamic Integration, i.e. making the ligand "disappear".

     Because this ligand is charged (-1), at lambdas different than zero
(when the ligand is already fading) the total system charge increases until
it is +1 when lambda=1.

     I am using 1 nm cutoff for the non-bonded interactions and PME. Should
I make something to account for this total system charge? Won't it induce
artifacts in my calculation?

thanks in advance,
Leandro Bortot

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