Analysis energy vdw and coulomb electrostatic for protein

User discussions
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1

Hi,

I’m totally beginner in Gromacs, but I’m trying calculation VDW and electrostatic energy for protein in water.
After MD simulation I got the following data such as:
Coul-14:Protein-Protein 48723.9 – 52.5646 128.039 (kJ/mol)
LJ-14:Protein-Protein 2911.89 – 63.8298 -132.528 (kJ/mol)

Then I tried calculation these interaction by using option: Coul-SR:Protein-Protein and LJ-SR:Protein-Protein and I get the following data:
Coul-SR:Protein-Protein -70583.7 – 202.553 390.266 (kJ/mol)
LJ-SR:Protein-Protein 300.207 – 150.764 -255.735 (kJ/mol)

Which of these values ​​look correct ? I want calculate vdw and electrostatic interactions only for protein.
What can be indicated by a high positive and high negative impact value for electrostatic interaction ? Whether the interactions in the protein are strongly attractive or repulsive? My another question is related with “Tot-Drift” - how I can interpreting this parameter ?

2

Decomposing interaction energies into the various components is physically meaningless. No force field is parametrized to give a sensible answer here (because there are no target data that can be used for parameter fitting). The sum of the interaction energy components may be meaningful, but only if the force field explicitly targets these quantities (e.g. CHARMM).