Hello all,
I am performing an MD simulation in AMBER. After analyzing trajectory for few ns, I have found the vdw interaction energy between solute and one solvent species (aromatic positive ion) is as high as ~+1000 kcal/mol. Generally, the negative interaction energy means high attractive force in case of electrostatic interaction. But, what does such huge vdw force signify?
Any help is appreciated.
Simply, a positive energy means a net repulsion with respect to the vdW term. There may be a large negative electrostatic value that offsets this positive value such that the total interaction energy is much lower.
Note that decomposing the energy in this way has no physical meaning; only total interaction energy *might* be useful, though most force fields are not parametrized in a way that makes this quantity real, either.
Such a large positive vdw interaction energy suually means that some atoms of the interacting species are too close to each other - which in turn usually means that there's something wrong with the parametrization or the setup of the system.
Simply, a positive energy means a net repulsion with respect to the vdW term. There may be a large negative electrostatic value that offsets this positive value such that the total interaction energy is much lower.
Note that decomposing the energy in this way has no physical meaning; only total interaction energy *might* be useful, though most force fields are not parametrized in a way that makes this quantity real, either.
Maybe you did not add the counter ions (usually Na+ and Cl-) to make your system neutral. You can just add the required number of counter ions or put everything in a water solution with a physiological NaCl concentration, e.g., for explicit solvent modeling, which is by far the best over implicit solvent modeling, at the cost of a larger simulation time. The vdw and electrostatic terms (weak bonds) of your pseudo potential should be always negative.
The number of counterions is not relevant, and there is no rule that any particular quantity should always be negative. Pairwise additive potentials can be positive (and in fact the short-range vdW potential often is), but again, the decomposition of such energy terms has no physical significance.
Justin Sir,
Thank you so much for clarifying my doubts. As you have suggested, I summed up both the electrostatic and vdw interaction energy and yes the total interaction energy is much lower (negative in most cases). The few positive values are now explainable with respect to my study and I have found such low positive values in literature also. That was a great help indeed.
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