[gmx-users] Peptide distance matrix

[Justin Lemkul]

On 4/15/13 11:08 AM, Steven Neumann wrote:
> 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?
>

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

-- 
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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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