mattwthompson / gromacs_signac_template

Template for MoSDeF- and GROMACS-centric project managed with signac

See generic signac template and a fork

Versions

signac-flow underwent significant changes from 0.4 to 0.5. The master branch will support versions 0.5 and newer but an older branch (flow-0.4) will be maintained to support version 0.4.

Installation

First, verify that each package in requirements.txt is installed. If not already installed, They should all be available via pip, conda, etc. The channels mosdef and glotzer or conda-forge are also required.

python setup.py install

Get started:

Initialize project:

python src/init.py

Build systems and perform energy minimization:

python src/project.py run initialize
python src/project.py run em  # energy minimization

Submit equilibration and production runs to the cluster (can also be run locally as above)

python src/project.py submit -o equil
python src/project.py submit -o sample

At any time you can evaluate the status of each job with:

python src/project.py status -d

Analyze system (here, simple timeseries plots of density)

python src/analyze.py

Look at the PDF file located in the workspace directory. It should look something like this:

gromacs_signac_template's Issues

Excessive dependencies

Currently mtools is a dependency, even though only the simple calc_density function is the only thing it is used for. Similarly, Tim's block_avg is used for one relatively simple function. Because neither is likely to have well-maintained releases, it's probably better to copy these functions directly into this project.