Error to generate xpm2ps output

User discussions
1

GROMACS version: 2020
GROMACS modification: No

Hi All,

I have an issue to visualize xpm data when I try to convert to eps format. The input format for xpm2ps is from gmx densmap output. here is the details,

gmx xpm2ps -f densmap_5u9d-WT_100.xpm -o densmap_5u9d-WT_100.eps -rainbow red
:-) GROMACS - gmx xpm2ps, 2020 (-:

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GROMACS: gmx xpm2ps, version 2020
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/crystalworkstation02/Syahrul/MD_simulation/100ns/WT/runWT_1
Command line:
gmx xpm2ps -f densmap_5u9d-WT_100.xpm -o densmap_5u9d-WT_100.eps -rainbow red

Program: gmx xpm2ps, version 2020
Source file: src/gromacs/fileio/matio.cpp (line 297)

Input error or input inconsistency:
Invalid XPixMap

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What should I do? Your help is highly appreciated. Thank you.

2

What does this mean? It supposed to be correct xpm file generated by gromacs itself. any clues?

3

This is a known bug and has been described in this forum within the last few days (please search before posting). Upgrade to 2020.3 and try again.

4

Thank you for the info.

Now I have upgraded to gromacs 2020.3. Yes the conversion is working.

Unfortunately, the graph scales (x- and y-axis) generated are badly overlapping (unreadable) refer attached.

Screenshot from 2020-07-15 11-54-42
Screenshot from 2020-07-15 11-54-421680×1050 201 KB

How can I fix this? your help is much appreciated. thank you.

5

There is a template file for conversion at /path-to-gromacs/share/top/ps.m2p. You can provide template file with -di option. Copy that file to current directory and adjust x-major/x-minor and y-major/y-minor, then supply with -di option while invoking gmx xpm2ps.

6

Hello
Sir, can you explain a little deep on adjusting the axes?
Thank You.