Thanks a lot Steven
On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/23/13 9:15 AM, Steven Neumann wrote: > >> Shall I specify one index group for two regions or 2 seprate? g_mindist >> asks just for one group. >> >> > If it only takes one, then you can only give it one. > > > would twice as cutoff would be sufficent to assess they do not interact? >> >> > Probably, maybe less, but that depends on the cutoff itself. Water > ordering can persist for up to 2.0 nm or so. > > -Justin > > >> On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann <s.neuman...@gmail.com >> >wrote: >> >> Thank you. >>> >>> Steven >>> >>> >>> On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 4/23/13 6:37 AM, Steven Neumann wrote: >>>> >>>> Dear Gmx users, >>>>> >>>>> >>>>> My protien has got some strong acidic and strong basic parts. I fold >>>>> and >>>>> unfold my protein with different temperaturss. I bserved high affinity >>>>> of >>>>> those regions towards each other, they are very close to each other >>>>> over >>>>> the simulation. >>>>> >>>>> How can I possibly check whether my two regions do not interact across >>>>> the >>>>> boundary conditions with such high affinity? >>>>> >>>>> >>>>> g_mindist -pi with a suitable index group. >>>> >>>> -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://vt.edu/Pages/Personal/justin> >>>> <h**ttp://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> >>>> <htt**p://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<h**ttp://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> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> >>> > -- > ==============================**========== > > 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
