# MiniOMM
```
_ _
_ __ ___ (_) _ __ (_) ___ _ __ ___ _ __ ___
| '_ ` _ \ | || '_ \ | | / _ \ | '_ ` _ \ | '_ ` _ \
| | | | | || || | | || || (_) || | | | | || | | | | |
|_| |_| |_||_||_| |_||_| \___/ |_| |_| |_||_| |_| |_|
```
A simple, HPC-friendly OpenMM wrapper for common-case MD runs, with minimal dependencies.
It works if it works for me.
[![PyPI version](https://badge.fury.io/py/miniomm.svg)](https://badge.fury.io/py/miniomm)
## Rationale
Developed to launch OpenMM runs on recent GPU-endowed machines,
including those with ppc64le architecture. This is because OpenMM can
currently be installed (also 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.
## Installation
In principle, the usual `pip install miniomm` should be sufficient.
However, you will need additional software:
* OpenMM and its Python interface
* Optionally, Plumed, openmm-plumed and its Python interface
See the [Wiki](https://github.com/giorginolab/miniomm/wiki)
for (somewhat site-specific) installation instructions.
## Syntax
For now, the syntax is only documented in the examples files. It
is a simple list of "keyword value" pairs, with sensible
defaults, and largely compatible with ACEMD.
## Features
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
* Checkpoints and restarts are enabled out of the box
* Plumed, if openmm-plumed is installed
* Tested on Linux x64 and ppc64le, with and without NVIDIA GPUs
Does not support
* Restraints of any kind
May support in the future, given sufficient interest
* Any feature provided by OpenMM, e.g. custom potentials.
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.
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资源分类:Python库 所属语言:Python 资源全名:miniomm-0.1.2.tar.gz 资源来源:官方 安装方法:https://lanzao.blog.csdn.net/article/details/101784059
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miniomm-0.1.2.tar.gz (20个子文件)
miniomm-0.1.2
PKG-INFO 3KB
miniomm.egg-info
PKG-INFO 3KB
SOURCES.txt 390B
entry_points.txt 46B
top_level.txt 8B
dependency_links.txt 1B
bin
sbatch_many 538B
pyproject.toml 109B
tests
import.py 37B
miniomm
main.py 2KB
miniomm.py 9KB
util.py 5KB
namdxsc.py 1KB
reporters.py 6KB
__init__.py 143B
namdbin.py 1KB
config.py 2KB
unused.py 352B
setup.cfg 779B
README.md 2KB
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