[gmx-users] average trajectory

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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