[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.


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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