This information is then binned into a probability matrix and normalised. It does this by identifying a reference atom, usually the phosphorous atom, and calculating a distance vector between each reference atom to determine the closest lipid. For each frame, Membrainy is looking to see which lipids are neighboured to each other. Two files should now exist in your current working directory: entropy.agr, and entropy_scaled.agr. It has also identified the reference atoms, with atom type PO4. gro file and determined the system contains two lipid types: POPC and POPE. This is not required to run the analysis however.
#XMGRACE FOR WINDOWS SOFTWARE#
You will also need to have the software "xmgrace" installed on your system in order to view the output plots. editconf_mpi) then please add the argument "-g_suffix _mpi" with every step in this tutorial, replacing "_mpi" with your chosen suffix. If you used a suffix for all gromacs binaries (e.g. It also assumes that your GROMACS binaries have typical names (e.g. Membrainy assumes that you have GROMACS currently installed and located within your classpath. Firstly, you will need to download the tutorial files here (171Mb).Ī few things to note beforehand: Please use the latest version of Membrainy. This tutorial should guide you through the basic usage of Membrainy, as well as analysing some test systems and understanding the output graphs.