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Task #2758

Modernize genconf

Added by Joe Jordan 9 months ago. Updated 9 months ago.

Status:
New
Priority:
Low
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
simple
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Description

The genconf utility is still cast in the c-style format. It should be migrated to work in the TrajectoryAnalysis framework. A minimal step in this direction should be to change the t_topology instantiation to a gmx_mtop_t as this will remove the need for many of the variables in the main function. A flag for modifying a .top file should also be added so that other tools, such as insert-molecules, can expect a well-formatted [ molecules ] section.

History

#1 Updated by Mark Abraham 9 months ago

Joe Jordan wrote:

The genconf utility is still cast in the c-style format. It should be migrated to work in the TrajectoryAnalysis framework.

Wearing my devil's advocate hat, what has genconf to do with trajectory analysis?

A minimal step in this direction should be to change the t_topology instantiation to a gmx_mtop_t as this will remove the need for many of the variables in the main function. A flag for modifying a .top file should also be added so that other tools, such as insert-molecules, can expect a well-formatted [ molecules ] section.

Can you elaborate, please?

#2 Updated by Joe Jordan 9 months ago

Wearing my "the devil made me do it" hat, that is a typo because I was not paying attention when I wrote this. I meant to write ICommandLineModule.

As to the second point, it was also a mistake in what I wrote. I meant that it would already get genconf most of the way there to being an ICommandLineModule to use TopologyInformation.fillFromInputFile() since that will give the the atoms, x, v, and box, which are all needed by genconf.

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