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