As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. Shahid Nayeem
On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: > >> Thanks. But Does that mean that I should look in pullf.xvg of each window >> and see whether the value is converged or not. If not then I should extend >> the simulation. >> > > I've already made numerous suggestions. The value in pullf.xvg is a > consequence of the nature of the system. Looking at the interactions > between your proteins, the stability of those proteins, etc. is far more > informative, like you would for any simulation (even those that do not make > use of the pull code). > > > -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> >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
