Re: [AMBER] Using average frame for nmode entropy calculation?

From: David A Case <>
Date: Sun, 28 Mar 2021 08:37:30 -0400

On Sat, Mar 27, 2021, Liao wrote:

>I’ve been comparing my entropy results from Quasi-Harmonic calculations
>and normal mode calculations, both from 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?

I have to guess here, but your quasiharmonic calculations are probably only
computing a few of the low-frequency modes, whereas the normal mode
calculations are getting all of them. If that is the case, you are getting
tons of contributions from high-frequency modes in the normal mode case,
which will indeed approximately cancel.

>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.

I'm not sure what you mean by "takes in only a average frame".
Quasiharmonic calculations average over the entire trajectory to get a
estimate of the effective force constants.

For normal modes, the results will not vary a lot from snapshot to snapshot.
You can run some tests to see how many frames you need to analyze to get a
good average -- that will vary from system to system.

...good luck...dac

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Received on Sun Mar 28 2021 - 06:00:07 PDT
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