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-boun...@maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mark.j.abra...@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.n...@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-boun...@maillist.sys.kth.se >>on >> behalf of Hannes Loeffler" >> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of >> hannes.loeff...@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.n...@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 >> >> >> >> >> >> >> > >> >-- >> >Gromacs Users mailing list >> > >> >* Please search the archive at >> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >posting! >> > >> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> >* For (un)subscribe requests visit >> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.