[gmx-users] Peptide distance matrix

[Steven Neumann]

Thank you for this.

Steven

On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists