miniomm 0.0.11

A simple OpenMM wrapper for common-case MD runs

MiniOMM

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A simple, supercomputer-friendly OpenMM wrapper for common-case MD runs, with minimal dependencies.

It works if it works for me.

Rationale

Developed to launch OpenMM runs on recent GPU-endowed ppc64le machines. OpenMM can currently be installed via Conda, but several related packages (such as mdtraj) cannot. MiniOMM aims to provide a "minimal working" environment for MD runs without requiring C++ or Python coding.

Features

The script is designed to be idempotent, that is, you may stop and restart it repeatedly, and it will progress until the end of the simulation. This may be convenient for time-limited batch systems.

Supports

• NVT (constant volume) production simulations with PME electrostatics and explicit solvent
• NPT (constant pressure) equilibration
• Runs pre-built systems in AMBER (prmtop) and CHARMM (psf) formats
• Restarts are enabled out of the box