Dr. Case
Thanks so much for the reply.
Here is a sample input file I feed into cpptraj, where 49.0 means the DNA molecule at length 49.0 A0, and is the same for all the other lengths:
parm strip.49.0.mbondi3.prmtop
trajin strippedtraj.49.0.crd
rms first :1-24&!.H=
average crdset 49.0.average
createcrd 49.0.nc
run
crdaction 49.0.nc rms ref 49.0.average :1-24&!.H=
crdaction 49.0.nc matrix mwcovar name 49.0.mwcvmat :1-24&!.H= out 49.0.mwcvmat.dat
runanalysis diagmatrix 49.0.mwcvmat out 49.0.evecs.dat vecs 20 name 49.0.myEvecs nmwiz nmwizvecs 20 nmwizfile dna.49.0.nmd nmwizmask :1-24&!.H= thermo outthermo thermo.49.0.dat temp 300.0
I used a total of 15 configurations corresponding to the lengths 49, 52, 58, 63, 69, 76,81, 86, 90, 93, 100, 102, 104, 106 plus the normal length (all in Angstrom).
My system is a dna of 12 basepairs, and I have attached a sample prmtop file for the length 49 A0. in the input file, mask :1-24&!.H= corresponds to all the residues of the DNA molecule except hydrogen atoms.
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?
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 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?
Thanks in advance
Ramin
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, July 19, 2017 7:33:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] problem Finding entropy
On Wed, Jul 19, 2017, Ramin Salimi wrote:
>
> To calculate the configurational entropy, I used quasi-harmonic
> analysis. However, the entropy for all the elongations showed pretty
> much the same number, only differing in the digits after decimal.
I think we would need details about how you did the quasiharmonic analysis:
how many snapshots did you use? (And how big is your system)?
>
> My guess is that it is calculating the entropy of the constraining
> force, because in all the production runs corresponding to different
> lengths, I have employed the same input files with the restraining
> constant k=100 to keep the molecule in that particular extension.
Quasiharmonic analysis just looks at the fluctuations about the average
structure, and just uses coordinates and masses as inputs. It has no idea
about whether you have restraints or not.
>
>
> My second question is why do I see translational, vibrational,
> rotational entropy contributions listed in the thermo.dat file along
> with the total entropy while I have already did rms to the first frame,
> find the average, and then rms to the average structure to REMOVE THE
> GLOBAL TRANSLATIONS AND ROTATIONS. I was expecting only vibrational
> entropy???
The thermo.dat analysis calculates translational and vibrational entropies
using the rigid-rotor model (using the average structure). So the
translational entropy should be the same for all extenstions, since you have
the same molecule. You may choose to ignore the rotational entropy if you
wish.
>
>
> My third question is when we are trying to find the entropy, the number
> of eigenvectors in front of "vecs" in the diagmatrix command should be
> the same as the number of atoms in the mask whose average structure
> was computed a few steps earlier. Is that right? Because my intuition
> says to find the entropy, we should take into account all the degrees
> of freedom except hydrogen atoms for example in a DNA molecule, or only
> backbone atoms in protein systems?
The only straightforward method to relate quasiharmonic calculations to
thermodynamics is if you choose all atoms. There are some empirical relations
that relate calculations on subsets of atoms to the full calculation, but they
are unlikely (in my view, anyway) to work for things like stretched DNA.
First thing is to figure out why you keep getting the same answer for
different geometries of the DNA. Be aware that you will need *lots* of
sampling and long trajectories to get converged results.
....dac
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Received on Wed Jul 19 2017 - 19:30:03 PDT
