Out of interest, I would like to know who has reported and for what reason a set of quantitative results using the total energy of an MD study? That is, the total energy reported at the end of the .log file from a Gromacs simulation.
Besides seeing whether the total energy has converged during a simulation (as you would do with temp and pressure and any structural changes lipid bilayer surface area), I don't use this value for quantitative or qualitative reports. I have always relied on thermodynamic techniques e.g., umbrella sampling, meta-dynamics, BAR & CGI.
Someone once told me why you should not use total energy. But that was many years ago and I can't remember.
Some thoughts on this topic would be very appreciated.
Thanks
The total energy is not useful for much of anything aside from proving that the simulation was physically valid (e.g. there is no systematic drift in the value). It tells you nothing of scientific importance. The potential energy is a force field-specific quantity; the energy of the same exact configuration of a system under a different force field will be different, and neither of those quantities is a free energy (which is what you get from umbrella sampling, BAR, etc). The kinetic energy is independent of the force field, of course, so the discussion of total energy relevance really is a discussion of the potential energy.
The total energy is not useful for much of anything aside from proving that the simulation was physically valid (e.g. there is no systematic drift in the value). It tells you nothing of scientific importance. The potential energy is a force field-specific quantity; the energy of the same exact configuration of a system under a different force field will be different, and neither of those quantities is a free energy (which is what you get from umbrella sampling, BAR, etc). The kinetic energy is independent of the force field, of course, so the discussion of total energy relevance really is a discussion of the potential energy.
Thanks, Justin.
Is there anything to be said about the comparison between potential energies of two systems, not so dissimilar from one another? A comparison not across different force fields or against experimental techniques?
I would not give a lot of credibility to comparing potential energies; there is no entropic term so it is not a free energy. Therefore, it really doesn't tell you anything reliable about the relative population or thermodynamic favorability of a given state.
One way of using total potential energies is an interpretation of time-resolved Stokes Shift spectra (e.g. http://dx.doi.org/10.1021/ct9001416). Another that comes to my mind is the calculations of the reorganization energies upon charge transfer in the context of Marcus' theory (e.g. http://dx.doi.org/10.1021/jp901888r).
The total energy reported at the end of MD simulation is hardly useful as Justin said
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