Got it (cool :)), Thank you!!! Best! Xueming On Wed, Jun 8, 2011 at 1:15 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > XUEMING TANG wrote: > >> Hi Justin >> >> Sorry I did not explain clearly. I apply position restraint to the head >> group of surfactant molecules and let all others (solvents and tail of >> surfactants) run freely. I am concerning about how long I should restraint >> the head group of surfactant molecules. If only concerning the solvent >> molecules, 10ps is enough for water to relax. But if concern the tail of the >> surfactant molecules, how to calculate the time of restraint (100ps, >> 500ps...). I guess 500ps position restraint will be enough? Is there any >> problem if I restraint the head group of surfactant micelle too long? >> >> > I doubt you can restrain anything too long. If all the relevant > thermodynamic observables have converged (T, P, energy, etc), then your > restrained equilibration is probably sufficient. Once you remove the > restraints, you'll have to assess some structural properties of the micelle > to know if it is equilibrated before collecting data. Maybe density, size, > etc. > > -Justin > > Thank you and have a nice day :P >> >> Best! >> Xueming >> >> On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> XUEMING TANG wrote: >> >> Hi there >> >> I put a SDS Spherical micelle in solution and want to apply >> position restraint before mdrun. Here I have a question: For >> macromolecules like micelles, should the position restraint >> apply to not only the water molecules (and ions) but also to the >> surfactant molecules in the micelle? If it is also for the >> surfactant molecules, how to calculate the position restraint >> time in this case. >> >> >> Why would you restrain the solvent? That basically prevents >> equilibration from happening. Then, if you restrain the solvent and >> surfactant, you truly accomplish nothing. >> >> Likely the best course of action is to restrain the surfactant >> molecules, while allowing everything else to move freely. Then, >> remove all restraints and equilibrate a while longer. >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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 >
-- 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
