And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written:
This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... Steven On Mon, Apr 15, 2013 at 4:24 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you for this. > > Steven > > On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > On 4/15/13 11:08 AM, Steven Neumann wrote: > >> > >> On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>> > >>> > >>> On 4/15/13 10:06 AM, Steven Neumann wrote: > >>>> > >>>> > >>>> On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On 4/15/13 9:59 AM, Steven Neumann wrote: > >>>>>> > >>>>>> > >>>>>> > >>>>>> Dear Gmx Users, > >>>>>> > >>>>>> I want to calculate a distance matrix of each amino acid (1, 2, > ...25) > >>>>>> averaged over simulation time with all amino acids. So matrix of > >>>>>> 25x25: > >>>>>> > >>>>>> 1) is there a tool which can do this or just the use of g_dist fof > 600 > >>>>>> (25x25 - 25) times? > >>>>>> 2) Would you recommend any nice visualisation tool (bioinformatic > >>>>>> software) to obtain colorful matrix? > >>>>>> > >>>>> > >>>>> g_mdmat does all of this. > >>>>> > >>>>> -Justin > >>>>> > >>>> > >>>> Thank you. As far as I see it does minimum dostance matrix and I wish > >>>> to have all distances averaged over the simulation time. Any advices? > >>>> > >>> > >>> So you want a per-atom matrix rather than a per-residue matrix? I > >>> suspect > >>> some quick hacking of g_mdmat would do that, but I don't know of any > tool > >>> that does so out of the box (nor would your original approach with > >>> g_dist, > >>> since it works on residue COM, not per-atom, unless you make groups for > >>> every single atom). > >>> > >>> -Justin > >> > >> > >> Thanks. I wish to have a distance matrix over the simulation time > >> per-central carbon atom of each residue. shall I specify one index > >> group with all central carbon atoms or 25 different index groups each > >> with Calpa? > >> > > > > All C-alpha carbons are in a default index group. Choose it when > prompted > > by g_mdmat and you'll get what you want. > > > > -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 > > > > ======================================== > > -- > > 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