Thank Justin so much !
On Sat, Feb 23, 2013 at 1:50 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote: > >> Dear all, >> >> I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is >> appropriate >> >> Can anyone tell me which value is appropriate for lipid membrane, for >> protein in water, for protein in lipid membrane ? >> >> > There is no absolute rule. The purpose of EM is just to get the > simulation system into a configuration that is sufficiently relaxed such > that dynamics don't implode. For sensitive free energy calculations and > normal mode analysis, you need the Fmax to be as low as possible. For most > protein systems, Fmax < 1000 is generally reasonable for normal MD, but > that's just an empirical observation. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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
