I’m trying to manually calculate the Coulomb & LJ interaction for a custom drug that I had modelled earlier using custom parameters, and verify them. When I checked the log for the 0th step after MD, it showed Coulomb 14 & SR values in the log file. Using the straightforward sum_i sum_j f * q_j * q_j / r, f = 138.4, didn’t give me the value shown in the log file.
This question has been asked earlier here, but I couldn’t find the 3.4.7 manual for the formula for Coulomb-14 explanation.
Another user has calculated it in this query, but the answer is vague to figure out the formula from the question.
Could you provide the manual on calculation of these energies? Thank you in advance.
You don’t say what doesn’t match. The Coulomb 14 term should be identical to the plain Coulomb formula you provided, potentially scaled by a constant if the force field has such a scaling.
The SR term will depend on the cut-off distance, type of electrostatics and Coulomb modifier used, which you all don’t specify. When using PME, it will also depend on the box dimensions.
Hi Hess. Apologies for the delay in response.
We have used coulombtype = Cut-off and coulomb-modifier = Potential-shift-Verlet in our gromacs simulation. We obtained Coulomb-14 = -1.45624e+03 kJ/mol and Coulomb (SR) = 7.80542e+02 kJ/mol for step 0 in our log file. The value that we obtain from the plain Coulomb formula above = -5423.2624652445875 kJ/mol.
There is a constant offset off the total potential with plain Coulomb cut-off for excluded pairs, identical to the reaction field correction. We have updated the reference manual in the 2022.1 release to document this.