[gmx-users] Peptide distance matrix

[Steven Neumann]

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.neumann08 at gmail.com>wrote:

> Thank you for this.
>
> Steven
>
> On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > On 4/15/13 11:08 AM, Steven Neumann wrote:
> >>
> >> On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>>
> >>>
> >>>
> >>> On 4/15/13 10:06 AM, Steven Neumann wrote:
> >>>>
> >>>>
> >>>> On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul <jalemkul at 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
> >
> > ========================================
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