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
