Hi Daniel
Thanks so much for the reply.
Well, I was planning to calculate the entropy based on the method by Schlitter:
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
What I was expecting, planning, to do was to get a matrix as the multiplication of mass and fluctuations matrices, then multiply it by some constant, then take the determinant, and then take the log of the determinant to get to the entropy. But from that file, evecs.dat, which supposedly carries the diagonalized matrix, how can someone add some other matrix to it or multiply it by some numbers, or how to take the log of that? Simply put, given that diagonalized matrix, evecs.dat, somebody should be able to do algebraic operations on it, like multiplication by numbers, taking the log, or the determinant, etc. But how should I do that?
Regards
Ramin
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Thursday, July 20, 2017 8:21:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] problem Finding entropy
On Wed, Jul 19, 2017 at 10:27 PM, Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
> question: why do I not see any such file as 49.0.myEvecs which supposedly contains the resulting modes? By the way, if we store the diagonalized matrix to 49.0.mwcvmat, what do we need 49.0.myEvecs for?
Do you mean the file '49.0.myEvecs' is not created? Are there any
warnings or errors from cpptraj? Writing the file can be useful if you
want to e.g. do a projection of the coordinates along those modes
later on.
> question: In the manual, it says that the thermo analysis calculates the entropy, and heat capacity using standard statistical mechanical formulas for an ideal gas. why should it be applicable to dna or protein systems? I mean how does this method find the entropy?
I recommend reviewing some of the literature on this - the idea has
been around a long time at this point. See e.g. Karplus and Kushick,
Macromolecules, 1981, 14, 325-332. Another good paper that delves into
some of the pitfalls of this method for calculating entropy is Chang,
Chen, and Gilson, JCTC, 2005, 1, 1017-1028.
> I was just expecting a diagonalized matrix which is the matrix multiplication of mass, and fluctuations, and openable then I would simply take its determinant. And finally multiply it by some other coefficients to get to the entropy based on the mathematical formulation I prefer.
>
> question: when I view 49.0.evecs.dat file, it says 1458 in the second line, but the number of the remaining lines seems to be bigger than that. I mean the total lines in the file is 4431 but when I multiply 1458*3, it gives 4374 which is not equal to 4431. Why?
The manual is your friend. The format of "evecs"/"modes" files is
given in section '28.10.10 diagmatrix' of the Amber 17 manual, page
660.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.lobos.nih.gov%2Flcb&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Cbc1ff2cc4f8544f5ce3708d4cf725ab4%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636361537432338191&sdata=OyD91hgARI7%2FYGbLrBxc3u8HO8v1UWsbhEs9BppShg4%3D&reserved=0
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Received on Thu Jul 20 2017 - 07:00:04 PDT
