[gmx-users] Thermodynamic integration

[Nash, Anthony]

Hi all,

I¹m looking for a guide on performing TI between a protein in its crystal
periodicity with a particular residue (state A), to the same system but
with a different residue (state B).

I¹m currently using
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free
_energy/01_theory.html as a guide, however this is more, if I understand
having read through it, on the presence-to-absence of methane in a water
solvent rather than a replacement with something else.

I haven¹t had too much luck googling and I¹m looking piecemeal through the
manual with little success.

Thanks
Anthony