Thank you! On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> Dear Gmx Users, Dear Justin, >> I run pulling of my ligand away from my protein. Then I used Justin perl >> script to extract distances for umbrella sampling windows between my ligand >> and crucial residue of my protein (Isoleucine). The number of hydrogen >> bonds between ligand and protein during the pulling is app. 3 at the >> begining, then 4 in some frames and then obviously zero (when ligand >> dissociated). >> Would you use the 1st frame as a starting window when number of hbonds is >> 3 or further window when this is number is 4? >> > > Assuming the first frame represents a fully-bound configuration, you > should start there. I'm guessing you're trying to determine the DeltaG of > binding for your ligand. If you define an arbitrary reaction coordinate, > you get an arbitrary answer. Starting and ending points dictate the value > of DeltaG (since it is a state function). > > > Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where >> interactions are via hydrogen bonds and hydrophobic interactions only? >> >> > > Most systems interact via hydrogen bonds and hydrophobic interactions. > Generally, 0.2 nm is a decent starting point, but should by no means be > viewed as any sort of universal standard. It worked for me in my tutorial, > it may not work for others. Consult the literature for similar systems and > proceed. If you find under-sampled regions along the reaction coordinate, > it is trivial to add a new window. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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