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. Shahid Nayeem
On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul <[email protected]> wrote: > > > shahid nayeem wrote: > >> My protein complex interface has a hydrophobic core and on each side of >> this core at the edge are two hydrogen bonds. The Hydrogen bond on one side >> is between Arg and Asp and another side it is between Arg and Glu. Its >> experimental Kd is in nanomolar regions. How should I decide the length of >> the simulation required in each window with this information. >> > > As you would any other system. Look for convergence of observables of > interest. Your PMF alone suggests insufficient sampling for these > simulations, so as I've said several times, you probably need longer > simulations to do so, but you can start by examining the physical > properties of each window. What you're looking for is up to you, based on > your knowledge of the system at hand. > > > -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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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