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
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