Where can I find the Definitions of the Energy Output Options?

User discussions
1

GROMACS version:
GROMACS modification: No
Hello,
I would like to use the gmx energy command to determine the total contribution of the electrostatic interactions to the total energy of a system as the simulation progresses but I am having trouble discerning what each option is referring to exactly. My guess is that “Coulomb-14” refers to the coulombic interactions between 1-4 pairs, “Coulomb-(SR)” refers to short range interactions and finally, “Coul.-recip.” is the reciprocal space contribution, presumably for the long range interactions.

  1. Is this the correct interpretation?
  2. Does summing only these three energies account for all the electrostatic contribution to the energy at that frame? (To be clear, I understand that this is different from the work required to charge a neutral system to the fully charged system, as that is not what I am after here.)
2

Yes.

Yes, however this quantity is not physically meaningful as no force field is designed to make it so.

3

Thank you for your quick response. Your answer to the second question prompts a follow up question.

  1. If I wanted to obtain the work required to (dis)charge a system, taking care to account for artifacts introduced by electrostatic interactions, could one use an alchemical transformation that slowly changes the partial charges to zero, or is the manner in which the partial charges assigned too far removed to give an sort of physical result? (I am working with the charmm 27 force field for lipids and proteins).
4

If you want to discharge an entire system, likely it will adopt entirely unphysical states that will render convergence essentially impossible.

Why? The lipid parameters are pretty bad there and were greatly improved in CHARMM36 a decade ago. Also note that there is no “CHARMM27” force field, it is CHARMM22/CMAP (also outdated with respect to CHARMM36m).

5

Thank you for the correction. Instead of my previous inquiry, if one wanted to determine the work required to discharge a solvated protein, not the entire system (solvent + counter ions + protein), could one use an alchemical transformation that slowly changes the partial charges for only that protein to zero, or is the manner in which the partial charges assigned too far removed to give an sort of physical result?

Thank you for your recommendation for using charmm 36.

6

You’re still going to run into a convergence problem, as waters attempt to sample unphysical locations around the protein and/or start to occupy previously inaccessible cavities. You’ll also need to apply position restraints to the protein to preserve its configuration. Whether any of that ends up being useful, I can’t say. Separation of LJ and Coulomb terms is not something that force fields are designed for, only total nonbonded energy.