[AMBER] Using average frame for nmode entropy calculation?

From: Liao <liaojunzhuo.aliyun.com>
Date: Sat, 27 Mar 2021 14:10:42 -0500

Dear AMBER users,
I’ve been comparing my entropy results from Quasi-Harmonic calculations and normal mode calculations, both from MMPBSA.py. A major difference in the results from I got was in the vibrational term, not talking about delta, just the total for each component of complex, receptor and ligand. Quasi-harmonic results were ~4 kcal/mol, while nmode was ~3500. The delta values are quite similar, but I’m also concerned about the entropy and total G energy values of the components themselves, so using quasi-harmonic method seems to be a problem to me?

The quasi-harmonic approach was attractive because of the much lower calculation cost. It doesn’t have a minimization stage, and it takes in only an average frame.
This led me to think that, is it appropriate to do the same with nmode? Still run the minimization, but use only a single average frame? Since they were setup by default differently, I assume there’s a reason why nmode doesn’t use an average, though I’m not sure of what it is.

Please help out, thanks very much.


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Received on Sat Mar 27 2021 - 12:30:02 PDT
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