[gmx-users] Thermodynamic integration

[Hannes Loeffler]

TI/FEP are appropriate when you have "small" changes between states.
Whether you delete/create all of a molecule or just part of it doesn't
matter that much.  So a relative simulation between a glycated and
non-glycated sounds quite reasonable to me.  Of course, this will become
increasingly more difficult with increasing chain length of
carbohydrates but you could do in additional steps if necessary.  What
is important is that you draw up a proper thermodynamic cycle to ensure
that you really calculate what you want to.

On Mon, 18 Apr 2016 11:06:40 +0000
"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:

> 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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