Dear all,
In thermal conductivity calculation of flexible methanol is it right to define the temp as we define for atoms.(NEMD)
I mean
compute ke all ke/atom
variable temp atom (c_ke)/(1.5).

And in the outputs (real units energy: kcal/mole) for flux calculation,should we multiply the number of atoms for dq or molecules?

Dear all,
In thermal conductivity calculation of flexible methanol is it right to
define the temp as we define for atoms.(NEMD)
I mean
compute ke all ke/atom
variable temp atom (c_ke)/(1.5).

And in the outputs (real units energy: kcal/mole) for flux
calculation,should we multiply the number of atoms for dq or molecules?

no. should there be a k_B in there somewhere?
this really is a problem that should be solved by sticking your nose into a
text book on MD and statistical thermodynamics and then comparing what you
need to do with what LAMMPS provides. this is *fundamental* and required
knowledge for any practitioner of these kinds of calculations and thus you
should not count on somebody giving you the answer. it may still be wrong
or not apply to your specific setup.