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,
--
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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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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