Re: [AMBER] Speed-up calculation of Entropy with MMPBSA

From: James Starlight <>
Date: Mon, 18 Feb 2019 14:16:41 +0100

Thanks for the idea!
Does the harmonic approximation generally faster compared to NMA
assuming same number of given snapshots?

пн, 18 февр. 2019 г. в 13:50, David A Case <>:
> On Mon, Feb 18, 2019, James Starlight wrote:
> >I have very fast calculation of
> >enthalpy contribution but on the stage of entrophy calculation (via
> >NMA or harmonic approximation) the calculations are stuck. Could you
> >suggest me something to improve performance of the calculations? Would
> >it be possible to use less interval with NMA for calculations of
> >enthropy with NMA?
> Yes: that is a common approximation. Start with fewer snapshots, and
> see how much a computed entropy varies among them. That will give you
> an idea of how many samples you will need to get a good estimate of the
> mean. Generally, the "instantaneous" entropy varies less than does the
> enthalpy.
> ....dac
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Received on Mon Feb 18 2019 - 05:30:05 PST
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