I have an expression which is very large and which has several sub-expressions with head Conjugate. What I want to do is simplify the Conjugate[...] sub-expressions without affecting other sub-expressions.
The first method I considered is was the Transformationfunctions option of Simplify. I wrote:
Simplify[expr,Transformationfunctions->{Conjugate}]
Well, Conjugate does indeed disappear, but the result is wrong. For example (with $Assumptions set so all variables are considered real)
FullSimplify[Conjugate[
t1 (2 Cos[(Sqrt[3] kx)/2] Cos[ky/2] + Cos[ky]) +
I t1 (-2 Cos[(Sqrt[3] kx)/2] Sin[ky/2] + Sin[ky])],
Transformationfunctions->{Conjugate}]
gives
t1 (2 Cos[(Sqrt[3] kx)/2] Cos[ky/2] + Cos[ky]) +
I t1 (-2 Cos[(Sqrt[3] kx)/2] Sin[ky/2] + Sin[ky])
The second method I considered is to use ComplexExpand //@ Conjugate. Since all the variables in my expression are declared real variables, Conjugate[expr] will become ComplexExpand //@ Conjugate[expr]. To make such this substitution, I could use search-and-replace and evaluate-in-place, but as I have said, the expression is large, so I don't want to do it that way. Instead I did the following:
largeexpr /. Conjugate -> ComplexExpand //@ Conjugate
But this did not work.
Here largeexpr is an expression containing sub-expressions with head Conjugate. For example,
Sqrt[t1^2]+Conjugate[
t1 (2 Cos[(Sqrt[3] kx)/2] Cos[ky/2] + Cos[ky]) +
I t1 (-2 Cos[(Sqrt[3] kx)/2] Sin[ky/2] + Sin[ky])]
So can anyone point out what I did wrong? Or suggest a better solution?

well, the "Conjugate" is indeed disappear, but the result is wrong....Can you add a small example of yourlargeexprhere that one can use? a small complete working examples always helps give you faster answers because the person who wants to help you will have something there to start with, and also helps clarifies the problem. (For example, to see what is it that is it that waswrongas you said in your statement above) – Nasser Dec 14 '12 at 11:43