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perm-md-count

Compute the Cumulative Number of Permeation of water molecules in a lipid bilayer in Molecular Dynamics simulations.

Quick start

Installation

Here are the steps to install perm-md-count in ~/Programs, but you can of course change the installation directory.

  1. Clone this repository on your computer.

    mkdir -p ~/Programs
cd ~/Programs
git clone https://github.com/ahardiag/perm-md-count.git

  2. Add the main script perm_lip.py to your python modules. For example, if you have a directory with some executable python script like /path/to/python/modules/, you need to link the main script on this program into this directory:

    ln -s ~/Programs/perm_lip/perm_lip.py /path/to/python/modules/

  3. Install the dependencies : This algorithm uses the python packages MDAnalysis, numpy and pandas. The best way to use perm-md-count is to run the executables in a conda environment with the librairies installed and the versions used during the development :

    conda env create --file "~/Programs/perm-md-count/perm_lip.yml" -n perm_lip
conda activate perm_lip

  4. Add the bash executable run_perm_lip.sh to your bash modules to run several analysis sequentially.

    ln -s ~/Programs/perm-md-count/run_perm_lip.sh /path/to/bash/modules/

Tutorial

To run the program, you need to provide an input file (by default parameters.in ) to your bash executable. In each line of this file - except comments and empty lines - are specified the parameters of the algorithm. All arguments in the same line must appear in the same order as in the following example:

#SUF            DATADIR REF               TRAJ                     FREQ    OUTDIRNAME  SUB 
SC8_6chnd_test3 ./      ref_SC8_6chnd.gro traj_SC8_6chnd_50ns.xtc  1000    test3/sub1  1

Then you just have to run the executable in a directory where you want to store results:

run_perm_lip.sh -f parameters.in

More information about the main python script can be obtained with :

perm_lip.py --help

MD trajectories

In principle, all formats that are readable by mdanalysis can be used. The membrane must be centered in the box. If several membranes are present in your system, just center your system on the membrane of interest. In order to delimit the membrane boundaries, the program consider only the lipids (phosphor atoms) located in a layer of 2MIN_DISP_MEMB=$60\AA$ around the central z-plane ($z = z_{box}/2$).

Parameters

Parameters Definition
SUF The keyword name, appended to output filenames.
DATADIR The relative path for the trajectory data.
REF The reference file (.pdb,.gro,.tpr) where resids are defined.
TRAJ The trajectory file (.xtc,.gro,.tpr).
OUTDIRNAME The name of the sub-directory to find outputs.
FREQ The sampling frequency (duration time in ns between two frames to analyze).
SUB The subdivision of the total number of water molecules. By default : 1. Useful for large systems and /or low RAM memory.

Outputs

The following files are writtent in ./outputs/OUTDIRNAME :

  • permeation_SUF.csv : a CSV file with permeation data
water_index resid time_per_frame(ps) time(frame) time(ns) duration(frames) direction permeations_tot
1843 2255 100 58 5.8 41.0 -1 0
... ... ... ... ... ... ... ...

Each line corresponds to a water permeation event, defined as a displacement of a water molecule from one leaflet limit (phosphorus atom of the bilayer) to the opposite leaflet. The corresponding events with periodic boundary crossings are excluded.

The first column has no column name, it is a simple index. By default, the program sort the permeation events with respect to the time of appearance, so the index dos not start from 0. The following information is extracted from the algorithm :

water_index          : the index of the water molecule in MDAnalysis
resid                : the residue index, given in the reference file.
time_per_frame(ps)   : same argument as FREQ (see above)
time(frame)          : the frame number which corresponds to the exit of the bilayer
time(ns)             : same event in nanosecond
duration(frames)     : the time spent in the bilayer/channel
direction            : the direction of the motion of the water molecule 
                       (+1 : from the lower to the upper compartment;
                        -1 : from the upper to the lower compartment)
permeations_tot      : the cumulative number of total permeations (in both 
                       direction)

permeation_SUF.log : a LOG file, text file with the name of the input files. Useful for post-processing.

  • limits_SUF.csv : another CSV file with the lipid boundaries mean trajectory

Other useful commands

Plot cumulative permeations timeseries

python plot_perm_tot.py perm_<SUF>.csv <SUF> --time_offset 10.0

More information about the main python script can be obtained with :

python plot_perm_tot.py --help

Outputs : It will generate XVG,PNG and PDF files with the number of permeations along time, and a SEL text file with the selection of the water molecule that have permeated. Useful to visualize in VMD.

Tests

cd tests
chmod u+x run_test1.sh
./run_test1.sh

Citation

If you use perm-md-count in your research, please cite the following article:

Hardiagon, A.; Murail, S.; Huang, L.-B.; van der Lee, A.; Sterpone, F.; Barboiu, M.; Baaden, M. Molecular Dynamics Simulations Reveal Statistics and Microscopic Mechanisms of Water Permeation in Membrane-Embedded Artificial Water Channel Nanoconstructs. J. Chem. Phys. 2021, 154 (18), 184102. https://doi.org/10.1063/5.0044360.