Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this?
Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/2/13 12:38 AM, Mohan maruthi sena wrote: > >> Hi all, >> I have system consisting of a peptide(alpha-helix), I want the >> peptide to be surrounded by magnesium ions(instead of water). How can i do >> this gromacs? How can I find the concentration of magnesium ions. just >> like >> in solution we have 0.5 Molar Mg+2 solution, My question how can find >> concentration by increasing number of ions. >> >> > I don't fully understand what you're trying to do, especially in the > absence of solvent, but I'll venture some simple advice. Concentration is > just the number of moles per unit volume. Simple unit conversion exercises > will tell you how many ions are needed to achieve whatever target > concentration you're looking for. > > -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