QwikMD creates a narrative file describing what it has done; this is filename.infoMD. The information here is *nearly* good enough to include in a journal article.
QwikMD creates a "setup" folder into which all necessary startup files are copied: parameter and topology files, constructed PDB and PSF, etc.
QwikMD creates a "run" folder which is the run-time input and output folder.
Current issues
- Error message when a stage is run — some sort of selection issue. This does not prevent the stage from running, but it probably causes the second issue.
- Run stages will not proceed automatically — Qwikmd does not seem to recognize when a stage has finished. SOLUTION: watch the log file ('tail -f run/Minimization.log', for example). When it is complete, re-load the .qwikmd file, and when the dialog box pops up, include the last stage. Then you should be able to start the next stage. Better solution: Once all the stages are prepared, create a shell script which will run all the configuration files sequentially.