[gmx-users] average trajectory

Erik Marklund erikm at xray.bmc.uu.se
Thu May 19 14:43:56 CEST 2011


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/




More information about the gromacs.org_gmx-users mailing list