[gmx-users] Thermodynamic integration

[Nash, Anthony]

From the site, “..or the free energy of a mutation of a side chain.”

I think this is what I am after. Many thanks for the link.

Anthony



On 18/04/2016 10:42, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Hannes Loeffler"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
Hannes.Loeffler at stfc.ac.uk> wrote:

>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/fr
>>ee
>> _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  
>> 
>> 
>> 
>
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