[gmx-users] Peptide distance matrix

[Justin Lemkul]

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

-- 
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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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