Dear Gromacs user how to solve error while running xpm2ps

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Dear Gromacs users,

I am trying to run gmx xpm2ps to convert and visualize a cluster.xpm file from my clustering to eps format. While running the following command:
“gmx xpm2ps –f clusterallfels.xpm –o clusterallfels.eps –rainbow red”

I get the following error:
“Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Positional argument ‘–f’ cannot be accepted. Perhaps you forgot to put a
hyphen before an option name.”

Does anybody knows how could I fix this?

Thank you in advance and appreciating any help

Kindly,
Lazaro

2

Hi Lazaro,

This seems like a copy-paste issue, where, .e.g, a pdf converter treats the - as a typographic cue to include an “em-dash”. – (note that the latter is ever so slightly longer than the -)

3

Let me know if replacing

by

gmx xpm2ps -f clusterallfels.xpm -o clusterallfels.eps -rainbow red

worked.

4

Hi Cblau indeed it runned but now it is showing me the following error:

Assertion failed:
Condition: mat.size() == mat2.size()
Combined matrix write requires matrices of the same size

Do you know what could be happening?

Also I am looking for information about criterias to select the right rmsd cutoff for the Gromos clustering. Do you know any materials or paper that mention kind of a set of rules for the selection of this cutoff?

Best regards

Lazaro