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. Rafael Giordano Viegas, Ingrid B. S. Martins, Murilo Nogueira Sanches, Antonio B. Oliveira Junior, Juliana B. de Camargo, Fernando V. Paulovich, and Vitor B. P. Leite Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.4c00034