[gmx-users] query about .xpm file

Mark Abraham mark.abraham at anu.edu.au
Thu Feb 22 14:36:56 CET 2007

> Dear Sir,
>      While viewing the trajectory of a 10ns MD
> simulation run , .xpm file is generated that can be
> converted into an .eps file , but the problem I am
> facing is in the time scale (X axis) in spite of
> exhibiting the scale it is giving a black bar, I used
> diifeerent permutation combination of -bx and -by ,
> the Secondary str file  improves, but no improvement
> in the time scale, rather  each time a black bar is
> displayed.
> How can I get the appropriate time scale?

I think a better approach for your problem than those suggested so far is
to go back and read the man page of do_dssp, where it will tell you about
an option that lets you sample the trajectory at a given frequency, rather
than use all the data. Using all the data seems to be giving you too many
x-tics to plot on the graph. This option is available for most of the
utilities that scan a trajectory.


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