[gmx-users] Thermodynamic integration

[Nash, Anthony]

Hi Mark,

I will give that a thorough read. I was wondering if you could possibly
comment on whether TI is an appropriate tool for calculating the free
energy difference between two states, A―> non-glycated side chain, and b―>
glycated side chain? Most examples given focus on the inclusion/exclusion
of some small molecule in some large system.

I have tried umbrella sampling and although my results are extremely
interesting, I’ve had to manipulate the initial systems to take it from a
crystal structure with defined periodicity in x-y-z dimensions, to a slab
in the x-y plane, and a water bath in the z plane.
 

Thanks
Anthony 




On 18/04/2016 11:53, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:

>Hi,
>
>Also you might consider pmx
>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
>generation. There is further work in the pipeline, so do get in touch with
>Bert if there's something of interest.
>
>Mark
>
>On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>> 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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