Embedded Files
Generating input files
Generating input files
Input files for benchmarking were generated with the CHARMM-GUI Membrane Builder, following the directions listed here. Changes may be necessary, depending on your purpose.
Benchmarking Bridges
Benchmarking Bridges
The same instructions listed on this page will work for benchmarking for the Opioid Project. However, instead of using the scripts provided there, you'll want to use benchmark.slu in this folder. The following table includes sample benchmarking data.
Production runs
Production runs
I have not yet needed to perform production runs on anything for this project. If you get there first, you'll want to use these scripts as a template and edit them to reference the appropriate files. In general, change references in the script from step3 to step5, step4.0 to step6.0, step4.1 to step6.1, and step5 to step7. You will also need to remove #SBATCH -A mcz3bqp from the file. You can reach out to me (Alec) if that doesn't work. If I end up doing production runs and forget to update this page, corrected scripts can be found here.
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