normal interaction energy

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1 year 3 months ago #8896 by shaukat_i
interaction energy was created by shaukat_i
Hello all,

I read that : interaction energies from simulations (LJ, Coul and total) are approximation and do nt mean anything. We should calculate free energies instead.
But how good are these energies in Martini CG since the system is of low resolution/ coarse?
Can we interpret anything from interaction energies?
Please guide.

SI

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1 year 3 months ago #8897 by vainikka
Replied by vainikka on topic interaction energy
It might be best to take a proper read on how and why certain interactions are modelled. "Molecular Modelling: Principles and Applications" by Andrew Leach, among many others, is a good place to start. You should be able to find some of the chapters in PDF-form online (and a used copies shouldn't be that expensive either).

You can also think more critically on your own statement: Suppose that LJ and Coulomb interactions are truly just fantasy (i.e. they don't mean anything) - do free energy methods rely on properties that require evaluating non-bonded interactions?

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1 year 3 months ago #8900 by shaukat_i
Replied by shaukat_i on topic interaction energy
OK. I will do. Thank you for reply.
But i read in gromacs tutorial (protein ligand md) that :
---The average short-range Coulombic interaction energy is -20.5 ± 7.4 kJ mol-1 and the short-range Lennard-Jones energy is -99.1 ± 7.2 kJ mol-1. It may be tempting to draw conclusions from the relative magnitudes of these quantities, but even though CHARMM was parametrized against explicit water interaction energies, decomposition of interaction energies further into these components is not necessarily real. There is no way to experimentally verify these quantities, so it is impossible to know whether they are meaningful. The total interaction energy, however, is useful in this case. That value (after propagating the error according to the standard formula for addition of two quantities) is -119.6 ± 10.3 kJ mol-1.

So, only the interaction energy between separate components are ok?

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1 year 3 months ago #8901 by vainikka
Replied by vainikka on topic interaction energy
Well, your question is already answered by the tutorial. The model gives you an estimation of the total interaction energy, and the accuracy of that depends, among many things, on how the force field was parameterized in the first place.

As I see it, the discussion you copied from Justin's tutorial is more related to the individual energy terms which the total interaction energy is comprised of. For example, it could be that the model you are using underestimates the electrostatic interaction but overestimates the LJ-interaction, resulting in an OK estimate. The point here is that you shouldn't draw conclusions on individual energy terms, but from the overall interaction.

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1 year 3 months ago #8904 by shaukat_i
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thank you for reply.
confusion was on the discussion in that tutorial.

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