Amber Parser

Version 0.0.1a

This is the parser for SANDER and PMEMD Molecular Dynamics codes in Amber. The official version lives at:

git@gitlab.mpcdf.mpg.de:nomad-lab/parser-amber.git

You can browse it at:

https://gitlab.rzg.mpg.de/nomad-lab/parser-amber

It relies on having the nomad-meta-info and the python-common repositories one level higher. The simplest way to have this is to check out nomad-lab-base recursively:

git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git

This parser will be in the directory parsers/amber of this repository.

Running and Testing the Parser

Requirements

The required python packages can be installed with (see python-common):

pip install -r nomad-lab-base/python-common/requirements.txt

Usage

Amber (SANDER/PMEMD) output files can be parsed with:

python AMBERParser.py [path/toFile]

Test Files

Example output files of Amber (SANDER/PMEMD) can be found in the directory test/examples. More details about the calculations and files will be explained in this README file.

Documentation

Installation of NOMAD Infrastructure

More information on the installation of NOMAD infrastructure can be found here