Thank you Justin! That helped a lot! Steven
On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Steven Neumann wrote: > >> Thank you Justin, now I get what you mean! >> As I understood I should pick just one frame untill 189 ps (when >> dissociation occured) - does it matter which one I will choose on the final >> binding free energy? >> > > The free energy minimum should (theoretically) be when the peptides are > still interacting, i.e. at time zero. Use this frame and base the spacing > off of it. > > > Then spacing should be 0.2 nm. Right? But how is it possible to do spacing >> like this from such results of summary_distances.dat: >> >> 189 0.5769072 >> >> 190 0.5753590 >> >> 191 0.5711223 >> >> 192 0.5719844 >> >> 193 0.5856807 >> >> 194 0.5886649 >> >> 195 0.5958101 >> >> ....... >> >> 211 0.7111782 >> >> 212 0.7322708 >> >> 213 0.7675126 >> >> ... >> >> 378 4.2101626 >> >> 379 4.1993918 >> >> 380 4.2223649 >> >> ...... >> >> 500 5.48839 >> >> Do you mean the approximate valueof 0.2 nm spacing? As it would be >> difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until >> e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until >> 5nm? >> >> > Choose approximate values. > > My protocol of uneven spacing was necessary to refine the energy minimum > for the suitable data for the paper. I kept the tutorial simple; you > should still achieve a reasonable result. Uneven spacing is uncommon in > the literature, so I did not want to give anyone the impression that it was > a standard protocol, leaving it as an exercise for the reader to understand > the paper and the motivation for uneven spacing. > > > -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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