[gmx-users] Peptide distance matrix

[Steven Neumann]

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?

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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