[gmx-users] average trajectory

[Tsjerk Wassenaar]

Hey,

If you can sum them, the only thing needed afterwards is updating the
color labels. Like per awk (dividing by two):

 awk -F\" '/#/{$4=$4/2}1' file.xpm

Cheers,

Tsjerk

On Thu, May 19, 2011 at 2:43 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Justin A. Lemkul skrev 2011-05-19 14.30:
>>
>>
>> Yulian Gavrilov wrote:
>>>
>>>
>>> Dear gromacs users,
>>> 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
>>> I want to make a distance matrix (*g_mdmat*) for the average trajectory
>>> of these 3 runnings.  *g_mdmat* gives an average  matrix for one trajectory,
>>> but I want to get it for the average trajectory.
>>> I tried to use *xpm2ps* to get average matrix, but in it I can only
>>> combine matrices (not to take an average matrix).
>>> Can I get an average matrix, or an average trajectory?
>>>
>>>
>>
>> I have thought about doing this myself, but have never attempted it.
>>  There is no Gromacs tool that will do such operations on .xpm files.  The
>> best I could figure would be to write an external script that:
>>
>> 1. Translates the .xpm matrix to numerical values based on the the header
>> information
>> 2. Takes the average at each position in the matrix
>> 3. Writes a new .xpm file
>>
>> -Justin
>
> I remember using imagemagick tools (composite?) to make average matrices
> from xpm files. I don't remember exacly how I did it though, and it may have
> required hacking the palette in the xpm files before combining them.
>
> Cheers,
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands