[gmx-users] Peptide distance matrix

[Justin Lemkul]

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

-- 
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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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