PackMem
To download the full software, go to :
- Visit our github deposit or clone it directly using :
git clone https://github.com/rogautier/packmem.git - Download PackMem
If you use and publish results using PackMem please cite :
R. Gautier, A. Bacle, M. Tiberti, P. Fuchs, S. Vanni and B. Antonny. PackMem: a versatile tool to compute and visualize interfacial packing defects in lipid bilayers. 2018.
Tools
You will find here some tools to facilitate the use of PackMem and associated analysis.
Run PackMem
Bash script that runs PackMem on a molecular dynamics trajectory. The script enables to run in parallel the three types of defects on multiple PDBs. You will first need to generate multiple PDBs from your MD simulation (following our best practices advice). Download
Statistical Analysis Script
R script that computes the packing defect constant and plots the packing defect distribution of your simulation. Download
Parameter files
In this section, we gathered all the parameters files already available for PackMem. If your lipid is not available, there is a tutorial page to help you do it.
Example files
In this section, you find different archives (tar.gz): to generate PDB files, to visualize output files from PackMem and to obtain statistical analysis.
- MD files Archive with MD files computed with Gromacs 5.0.x This archive contains xtc file, tpr file, ndx file and gro (start and end) and a script file from a DOPC(85%)DOPE(15%) simulation (400ns frame saved each ns).
- PackMem output files Archive with an example of output files from PackMem tool with a PDB file.
- Statistical Analysis Archive with an example of statistical analysis using R script.
Contact
Comments, feedback, bugs: please send all remarks to: 