[gmx-users] average trajectory

Justin A. Lemkul jalemkul at vt.edu
Thu May 19 14:30:51 CEST 2011

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 
2. Takes the average at each position in the matrix
3. Writes a new .xpm file



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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