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littleworth
littleworth
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How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

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littleworth
littleworth
  • 1.7k
  • 9
  • 29

How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)

I was performing MD simulation for protein-ligand complex following GROMACS tutorial.

I compared the energy of two ligands (S1 and S2) to a protein, using GROMACS LJ-SR (Lennard-Jones Short Range) and Coul-SR (Coulombic Short Range) option.

Below is the plot.

enter image description here

As you can see the LJ-SR is complete opposite of Coul-SR. Are they expected to be the opposite? Which is more appropriate choice to represent real binding energy?