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

From: David A Case <>
Date: Mon, 18 Feb 2019 07:50:12 -0500

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


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Received on Mon Feb 18 2019 - 05:00:02 PST
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