[gmx-users] Peptide distance matrix

[Steven Neumann]

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?

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
>
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