pyLFDA 2.0

pyLFDA is a tool which allows analysis of pairwise lipid force distribution along with other functions such as curvature and diffusion.

pyLFDA

pyLFDA is a tool which allows analysis of pairwise lipid force distribution along with other functions such as curvature and diffusion. Our tools enables easy usage of different versions of Gromacs-FDA as the user is only required to specify the version and pyLFDA handles the rest. We provide 3 modes of usage for all properties -

• Average - Averages the property for each atom over all input frames.
• Framewise - Property values for a particular frame.
• Moving Window - Averages the property for each atom over a window of frames of specified size for all non overlapping windows possible.

pyLFDA has 3 different interfaces - GUI, CLI and Python package, each providing the same functionality while suiting your use case. We utilize force calculation done by Gromacs FDA and parse it into useful formats. pyLFDA also enable users to select the version of Gromacs FDA they require with one simple argument and it handles the rest for all future experiments.

Installation

This project works with Python on versions 3.5+, and on Linux, OSX and the Windows operating systems. To install:

pip install pyLFDA

Other requirements -

• GROMACS
• Numpy
• Scipy
• MDAnalysis
• Membrane Curvature

Force

pyLFDA provides plots of pairwise force on selected residue groups. Forces calculated are plotted along the z - axis which helps users understand how forces are distributed along the membrane.

Curvature

pyLFDA utilizes MDAnalysis and provides cross sectional plots along the x-y axis for the z-surface, curvature, gaussian curvature of the P atoms. We provide line plots for the bins containing the maximum and minimum values. Also, cross sectional force plots are provided which allows the user to find the correlation between forces on atoms and their curvature. Additional options include splitting the membranes into upper and lower membranes and changing the number of bins to divide the membrane cross section into.

bFactor

pyFDA allows user to create PDB files with bFactor calculated either for individual atoms or averaged for each selected residue group.

Diffusion

We use MDAnalysis to calculate MSD and diffusion over all the frames.

Usage

For each experiment run, the plots and files are saved in a folder specified by the -experiment_name argument. If not specified, the program generates a folder for the time of program run. If a new Gromacs FDA version is supplied, it is downloaded into a new directory and it utilized for all future experiments. Gromacs FDA generates a .pfa file as output which generally is time consuming and for this we provide an argument -pfa which can load this file and does not require FDA to run again. pyLFDA further parses this file into averaged and framewise version both of which can be loaded using -avg_pfa and -f_pfa arguments respectively if one needs to do additional experiments on the same simulation.

Command Line Interface

Command Line Interface for pyLFDA. Download pyLFDA_cli.py(download) from the releases and follow the instructions from below.

usage: pyLFDA_cli.py [-h] -v Version [-exp Experiment Name] -trr TRR Filename
                     -tpr TPR Filename -ndx NDX Filename -pdb PDB Filename
                     -gro GRO Filename [-pfa PFA Filename]
                     [-avg_pfa Average Parsed PFA Filename]
                     [-f_pfa Frameise Parsed PFA Filename] [-avg]
                     [-f Specific Frame] [-window Moving Window] -gr1 Group 1
                     -gr2 Group 2 [-force] [-curve] [-diffu] [-cluster]
                     [-split] [-bfac bFactor] [-xbins Num_xBins]
                     [-ybins Num_yBins]

Command Line Interface for pyLFDA

 required arguments:
  -v Version            Release version of Gromacs FDA to be used
  -trr TRR Filename     TRR file to be used
  -tpr TPR Filename     TPR file to be used
  -ndx NDX Filename     NDX file to be used
  -pdb PDB Filename     PDB file to be used
  -gro GRO Filename     GRO file to be used

optional arguments:
  -h, --help            show this help message and exit
  -exp Experiment Name  Name of the experiment. If not specified time-stamp of
                        experiment will be used
  -pfa PFA Filename     PFA file to be used. If PFA file is specified, FDA
                        wont run again
  -avg_pfa Average Parsed PFA Filename
                        Average Parsed PFA file to be used. If Average PFA
                        file is specified, FDA and PFA parsing wont run again
  -f_pfa Frameise Parsed PFA Filename
                        Frameise Parsed PFA file to be used. If PFA file is
                        specified, FDA and PFA parsing FDA wont run again
  -avg                  Calculate average forces for all frames
  -f Specific Frame     Calculate forces for a specific frame
  -window Moving Window
                        Calculate forces for a moving window
  -gr1 Group 1          Group 1 to be selected
  -gr2 Group 2          Group 2 to be selected
  -force                Calculate Force
  -curve                Calculate Curvature
  -diffu                Calculate Diffusion
  -cluster              Generate Lipid Cluster Plots
  -split                Split Calculations into Upper and Lower Membranes
  -bfac bFactor         Calculate B-factor. "atomwise", "groupwise".
  -xbins Num_xBins      Number of bins in x-direction
  -ybins Num_yBins      Number of bins in y-direction

Graphical User Interface

The GUI offers the same functionality with the ease of a graphical interface. To download, either clone the repository and run pyLFDA.exe or click here.

Python Package

Detailed documentation and usage instructions for pyLFDA can be found in this example.