Molecular Dynamics Simulations Hemochromatosis

Hemochromatosis>>Task 8: Molecular dynamics simulations

Riddle of the task

Sorry, not this week. Too busy... Meanwhile you could go on a journey or quest: Journey Quest

Short task description

Detailed description: Molecular dynamics simulations

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

Diary of "trial and error"-hell...

Tipps for other groups:

• AGroS wants to run "scwrl" and not "Scwrl4" which is the name after the installation.
  • Solution: ln -s Scwrl4 scwrl

• Problems NVT!!! (Can not open file: *_nvt.tpr).
  • Solution: reduce to 16 cores (instead of 32)
    • Anybody tried 32 cores on the real runs??
      • Yes, tried and it worked in the real run. The --partition=inter queue still throws segfaults on the NVT run, though.. ;)

Current "test" state:

• Run min I: solvent & fixed protein(SD) ...finished
• Run min II: solvent & fixed backbone(SD) ...finished
• Run min III: solvent & fixed backbone(CG) ...finished
• Run NVT ...finished
• Run NPT ...finished
• Production run ...terminated after the 2 hour limit (without errors)

Starting mutation runs:

• Wildtype (status: still pending...)
• R224W (status: still pending...)
• C282S (status: still pending...)

...approximated start: Sunday or Monday -.-