About MOSAICS

MOSAICS is a collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems. These tools focus on the efficient computation of spatially resolved time-averaged lipid observables like the membrane thickness, lipid tilt angle, residence time, etc. However, other types of analysis are possible; see "mosaics_user_manual.pdf" for details. To ensure peak performance, we have programmed MOSAICS in C++ and implemented a trajectory reading framework called the MOSAICS Analysis Template, or MosAT for short. MosAT reads individual trajectory snapshots into memory, thus reducing memory requirements and enabling the analysis of very large trajectory files. MosAT is also programmed to distribute the workload across available computing cores. As such, each MOSAICS tool is fully parallelized.

Software/hardware requirements

• A computing cluster
• A recent version of Open MPI
• A c++ compiler like g++
• A c++ compiler with MPI support like mpic++

Installation instructions

Here we provide a brief overview of the installation process. We note that a more detailed description is provided in the user manual.

 cd MOSAICS
 mkdir build
 export MPI_CPP_COMP="mpic++"
 export CPP_COMP="g++"   
 sh install_commands

Alternatively, the user can try the following CMake recipe:

 cd MOSAICS
 mkdir build
 cmake src/MosAT/programs/ -S . -B build/
 cmake --build build/

Getting started

Detailed instructions for using each tool can be found in the user manual, i.e., "mosaics_user_manual.pdf". Note that we provide a sample trajectory in the "examples/membrane_thickness/" folder so the user can reproduce much of the analysis shown in the user manual. Example input files, such as selection cards and parameter files, are also included in the "examples/" folder. We also include scripts, mainly used for ploting grid data, in the "scripts/" folder.

Code layout

The MOSAICS source code is organized as follows:

• Source code for MosAT-based tools is located in "src/MosAT/"
• Source code for non-MosAT-based tools is located in "src/other_tools/"
• Header files encompassing the MOSAICS library are located in "src/headers/"
• Files sourced from MDTraj that are used for reading GROMACS trajectories are located in "src/xdr/"
• Routines sourced from the GROMACS MD simulation package are located in "src/gmx_lib/"

License

MOSAICS is licensed under the BSD-3-clause license, and additional details may be found in the "LICENSE" file; see also for licensing info regarding code sourced from GROMACS and MDTraj.

Citing MOSAICS

Please cite Bernhardt N, Faraldo-Gómez JD, MOSAICS: A Software Suite for Analysis of Membrane Structure and Dynamics in Simulated Trajectories, Biophysical Journal (2022), doi: https:// doi.org/10.1016/j.bpj.2022.11.005.

BibTeX

@article{BERNHARDT2022,
    title = {MOSAICS: A Software Suite for Analysis of Membrane Structure and Dynamics in Simulated Trajectories},
    journal = {Biophysical Journal},
    year = {2022},
    issn = {0006-3495},
    doi = {https://doi.org/10.1016/j.bpj.2022.11.005},
    url = {https://www.sciencedirect.com/science/article/pii/S0006349522009031},
    author = {Nathan Bernhardt and José D. Faraldo-Gómez},
}

Feedback

Please report bugs identified within the source code and other errors like typos found in the user manual using the issues feature. Other comments and suggestions are always welcome. Thank you for your help.

Troubleshooting

Are you having difficulty using MOSAICS? Not certain how to prepare your simulation for analysis? Need help adding an unrecognized lipid type or other basic inputs parameters? No problem! Please post your questions in the issues section.