I trying to calculate the configurational entropy (-TdelS) of the protein-ligand complex with the help of Interaction Entropy (IE) method. Can anybody give me the idea for how to do that or please give the AMBER script for calculating the same?
During the process of deriving the so-called entropy, in fact, ΔQ/T can not be turned into dQ/T. That is, the so-called "entropy " doesn't exist at all.
The so-called entropy was such a concept that was derived by mistake in history.
It is well known that calculus has a definition,
any theory should follow the same principle of calculus; thermodynamics, of course, is no exception, for there's no other calculus at all, this is common sense.
Based on the definition of calculus, we know:
to the definite integral ∫T f(T)dQ, only when Q=F(T), ∫T f(T)dQ=∫T f(T)dF(T) is meaningful.
As long as Q is not a single-valued function of T, namely, Q=F( T, X, …), then,
∫T f(T)dQ=∫T f(T)dF(T, X, …) is meaningless.
1) Now, on the one hand, we all know that Q is not a single-valued function of T, this alone is enough to determine that the definite integral ∫T f(T)dQ=∫T 1/TdQ is meaningless.
2) On the other hand, In fact, Q=f(P, V, T), then
∫T 1/TdQ = ∫T 1/Tdf(T, V, P)= ∫T dF(T, V, P) is certainly meaningless. ( in ∫T , T is subscript ).
We know that dQ/T is used for the definite integral ∫T 1/TdQ, while ∫T 1/TdQ is meaningless, so, ΔQ/T can not be turned into dQ/T at all.
that is, the so-called "entropy " doesn't exist at all.
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Why did the wrong "entropy" appear ?
In summary , this was due to the following two reasons:
1) Physically, people didn't know Q=f(P, V, T).
2) Mathematically, people didn't know AΔB couldn‘t become AdB directely .
If people knew any one of them, the mistake of entropy would not happen in history.
Please read my paper and those answers of the questions related to my paper in my Projects.