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Bug #425

x2top defunct?

Added by Justin Lemkul over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

I was checking out the latest git version of the code to see if the issues with x2top -nopbc had been resolved, and it looks like x2top might be completely nonfunctional. There are no .n2t files in the new /share/top directory structure, so my guess is that x2top would be crippled. Is this intentional? I can generate topologies with my own custom .n2t files, however. If there are not supposed to be any .n2t files in the distribution, perhaps when the program fails with a fatal error it should suggest to the user that an .n2t file is needed, or perhaps it could be listed as a required input. Right now the fatal error points to the Errors page on the Gromacs site, but there's not any useful advice there.

The main issue is that x2top in the 4.0.x series hangs without the use of -nopbc, so I would suggest at least making this option the default setting. Some time ago, I made note of this issue on the wiki, but couldn't find a bug report.

There is also a minor typo in the description of the -ff option: "selcection" should be "selection" :)

History

#1 Updated by David van der Spoel over 9 years ago

Made x2top (very) slightly functional again. Still the n2t files need some work.

Also fixed the typo :).

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