Dr. Case
Awesome, sounds like a plan.
will do it.
As the final question, you said 4ns with 2000 snapshots shouldn't give convergence for entropy. why is that so? If the output file shows the energy converges by the end of the run, wouldn't that be enough? I mean, is convergence criterion any different for the entropy?
Regards
Ramin
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, July 20, 2017 10:16:47 AM
To: AMBER Mailing List
Subject: Re: [AMBER] problem Finding entropy
On Thu, Jul 20, 2017, Ramin Salimi wrote:
>
> Well, I was planning to calculate the entropy based on the method by Schlitter:
It's been a long time since this came up for me, but the entropy
calculation already done by Amber is more accurate than the Schlitter
approximation. See:
%A I. Andricioaei
%A M. Karplus
%T On the calculation of entropy from covariance matrices of the atomic
fluctuations
%J J. Chem. Phys.
%V 115
%P 6289-6292
%D 2001
It could be a good learning exercise to implement the Schlitter idea and make
comparisons for yourself, but you should first study the existing
quasi-harmonic code so that you understand what it is doing.
Note also that 4ns and only 2000 snapshots are almost certainly well below
what is needed to converge quasiharmonic entropies--but try some experiments
yourself. On the other hand, if the trajectories are not doing what you think
they should, that needs to be investigated. (It seems unlikely that the
strength of the restraint is very important, though.)
...dac
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Received on Thu Jul 20 2017 - 09:00:03 PDT
