And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze?
Steven On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann <s.neuman...@gmail.com> 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? > > Steven > >> >> >> -- >> ======================================== >> >> 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