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From: David A Case <david.case.rutgers.edu>

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 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?
*

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

Date: Sun, 28 Mar 2021 08:37:30 -0400

On Sat, Mar 27, 2021, Liao wrote:

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.

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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