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From: Liao <liaojunzhuo.aliyun.com>

Date: Sun, 28 Mar 2021 09:48:03 -0500

Thanks for the answer there,

So from what I see, MMPBSA.py is calling cpptraj and seems to be generating an average frame over all the selected frames, and doing the quasi-harmonic calculation on that single frame.

I guess now I’ll try to first manually generate an average in cpptraj, and use that single frame as the nmode calculation input to see what I get.

*> On Mar 28, 2021, at 7:37 AM, David A Case <david.case.rutgers.edu> wrote:
*

*>
*

*> 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 - 08:00:02 PDT

Date: Sun, 28 Mar 2021 09:48:03 -0500

Thanks for the answer there,

So from what I see, MMPBSA.py is calling cpptraj and seems to be generating an average frame over all the selected frames, and doing the quasi-harmonic calculation on that single frame.

I guess now I’ll try to first manually generate an average in cpptraj, and use that single frame as the nmode calculation input to see what I get.

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Received on Sun Mar 28 2021 - 08:00:02 PDT

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