On 11/06/2012 8:22 PM, Markus Kaukonen wrote:
Dear All,
Sorry to trouble you with the same question, but my question from last
friday was probably badly formulated, so I'll try again.
Assume our system consists of ten atoms (atom indexes 1-10).
It has two groups,
group A has atoms 1, 7, 9
group B has atoms 2-6, 8, 10
Is it possible (either during the run or by postprocessing)
to get the total energies associated to groups A and B (thus E_tot =
E_tot(A) + E_tot(B) )?
If not, what would be easiest strategy to hack this out? Would it be
g_energy or g_enemat or something else?
This is straightforward to do as far as non-bonded quantities go, but
requires planning when you construct your .mdp for either the original
run, or an mdrun -rerun. Look for energy groups in the manual.
Decomposing the bonded quantities will require you do some more tedious
work, e.g. zeroing parameters or removing molecules in the .top and
doing a rerun.
As Justin said, you will not be able to easily decompose the
reciprocal-space term for PME, and whether these sums mean anything is
doubtful.
Mark
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