High vdW energy (LJ-SR)

User discussions
1

Dear all,

After the calculation of (LJ-SR), could you please tell me if the vdW energy (average) around 200000 kJ/mol (positive) can be correct?

I appreciate your responses in advance.
Best

2

That seems a little high, but it could be possible. What is the error estimate associated with this quantity?

3

Thanks for your response.

The calculation includes 2 protein, 12 ligands and 500 lipids for four systems. Hence, aim was to compare results that are around 175000 to 200000 kJ/mol.

With this high positive quantity, is this still reasonable to compare results? (e.g. lower values are due to more vdW participation).

4

You cannot decompose nonbonded interactions into their components and make any reasonable conclusions. The total nonbonded energy (sum of LJ and Coulomb) may be useful if the force field has been parametrized in such a way that interactions have been explicitly calibrated. Beyond that, no, you cannot make any argument about strength of vdW interaction based on differences in LJ-SR, and it’s not a physically verifiable value.