ELViM: Energy Landscape Visualization Method

ELViM is a method for visualizing the energy landscapes of biomolecules simulations.

Requirements

We recommend the Conda package when installing the required libraries.

MDTraj

MDTraj is a python library that allows users to manipulate molecular dynamics trajectories. To install MDTraj using conda, execute the following command:

conda install -c conda-forge mdtraj

Numba

Numba is an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code. To install Numba using conda, execute the following command:

conda install numba

NumPy

NumPy is a library that allows operations with multidimensional array objects. To install NumPy using conda, execute the following command:

conda install numpy

Execution

The ELViM code runs with flags to control all possible parameters. To see the options, use: python ELViM.py -h

Example

To run an standard ELViM projection one only needs the ELVIM.py and the force_scheme.py available here, as well as the desired trajectory file.

python ELViM.py -f trajectory.pdb -o output.dat

Alternatively, for a xtc file you do required a topology file.

python ELViM.py -f trajectory.xtc -t topology.pdb -o output.dat

Analisys Notebook

A notebook illustrating basic visualizations analisys is available in Colab

Citation

Please cite the following papers when using ELViM:

1. Oliveira Jr, A. B., Yang, H., Whitford, P. C., & Leite, V. B. (2019). Distinguishing biomolecular pathways and metastable states. Journal of chemical theory and computation, 15(11), 6482-6490.
2. Viegas, R. G., Martins, I. B. S., Sanches M. N., Oliveira Jr, A. B., Camargo, J. B., Paulovich, F. V., & Leite, V. B. (2023). ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization.