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://www.lobos.nih.gov/lcb
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Received on Thu Jul 20 2017 - 06:30:02 PDT
