GitHub - ccaratelli/MD-scripts: Collection of scripts used during a molecular simulation project

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Collection of scripts used during a molecular simulation project

GPL-3.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 56 Commits
test		test
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
angle_bond.py		angle_bond.py
average_deltaE.py		average_deltaE.py
gauss_legendre.py		gauss_legendre.py
get_structural_param.py		get_structural_param.py
graph.py		graph.py
harmonic_oscillator.py		harmonic_oscillator.py
merge-traj.py		merge-traj.py
parse_pv.py		parse_pv.py
plot		plot
plotdeltaE.py		plotdeltaE.py
wrap_cell.py		wrap_cell.py

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Some scripts I used during a project during my PhD.

angle_bond.py - extracts bond and angle distributions to find values of a harmonic oscillator that replicates such distribution
harmonic_oscillator.py - generates a Boltzmann distribution of harmonic oscillators
merge-traj.py - trims and combines molecular trajectories, adds unit cell parameters in case of a npt simulation for processing with PLUMED
average_deltaE.py, gauss_legendre.py, plotdeltaE.py - perform the thermodynamic integration to determine pKa from the insertion-deletion simulations
get_structural_param.py, parse_pv.py - parses cp2k output to extract pressure, volume and unit cell parameters
plot - a simple perl command line interface for gnuplot

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Collection of scripts used during a molecular simulation project

GPL-3.0 license

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