Peyman Yamin wrote:
Thanks!
I had somewhere in my mind a memory of seeing an interactive g_energy some
time ago, but it could be another version of it or that place in my mind
would need a defragmentation! comments helped indeed anyway.
If group X is one molecule, you would know from it's energy, i.e. the sum of
interactions its atoms have with themself and with the surrounding solvent, a
plenty of useful things. It could, if analysed with an eye on physicochemical
nature of interactions and the resulting conformers, could give neat insights
in some cases. e.g. how would one find some attractors about a certain
arbitrarily defined size-related property, in terms of stability? I thought
if molecule X is tending to have some conformer with the least energy in
medium A, it would also be tending to have an alike conformer in some other
medium of the same nature to the first one.
In general, you can't just ignore entropic considerations here - that's
one reason for doing condensed-phase MD, rather than vacuum calculations
of some sort. MM forcefields are typically parameterized to reproduce
certain physical or quantum chemical computational observables. Unless
you can show a direct relationship between some of these and your
property of interest, then you're on very shaky ground using the MM
forcefield.
This is what I think, and, you might want to correct me of course.
But what I don't know now is if the tot-energy output from g_energy when one
chooses a certain molecule, is actually what I think it is, or it's
calculated in another way? How would I know?
"Total energy" in g_energy and the .log file is for the whole system. An
mdrun -rerun with a topology that's had most of its contributions
zero-ed out is one way to get your single-molecule total energy.
Mark
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