And also the main question to me is that I read the entropy the same number for all different elongations, just wanted to know what I did wrong. It don't make sense the entropy for the molecule with length 93 A0 be the same as with 50 A0
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Thursday, July 20, 2017 8:50:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] problem Finding entropy
Ramin, I am not sure I understand the question.
If you have the data, all you need to do is reading it into a program
you can write, and then manipulate it in any way you want.
Also, are you sure amber is not already implementing the Schiltter
method (or something very similar) for instance in MMPBSA.py ?
MMPBSA.py for sure reads the cov matrix and manipulates it.
adrian
On 7/20/17 9:46 AM, Ramin Salimi wrote:
> 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
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jul 20 2017 - 07:00:06 PDT
