[gmx-users] Thermodynamic integration

[Hannes Loeffler]

A good starting point is http://www.alchemistry.org/ which has quite a
lot of detail on relative alchemical free energy simulations (not only
TI).

On Mon, 18 Apr 2016 09:27:02 +0000
"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:

> 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  
> 
> 
>