Re: [AMBER] About calculating entropy

From: Hannes Loeffler <>
Date: Thu, 31 Oct 2013 14:03:28 +0000

On Thu, 31 Oct 2013 13:47:21 +0000
Tivani Mashamba <> wrote:

> Hi Jason,
> When you say even 5000 frames won't be enough, do you mean that it is
> not worth calculating entropy for a 5ns system?
> Kind regards
> Tivani

I don't think it is (just) a matter of the number of frames. It is
really a question of how well your simulation captures the collective
motions which are well known to converge very slowly. The way how
MM-PBSA simulation appear to be typically run, i.e with just a few ns of
simulation, probably do not lend themselves to QHA.

Also see the thread "huge values for the vibrational entropy from
ptraj" from today.
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Received on Thu Oct 31 2013 - 07:30:19 PDT
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