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d-clust

This Python script uses the DADApy library to perform a DPA clustering analisis based on temporal traces of dihedral angles obtained from molecular dynamics trajectory.

d-strings

A python script to perform strings optimizations in Amber, using dihedrals as collective variables.

feneb

A tool for performing nudged elastic bands simulations on the free energy surface using Amber .nc files.

hybrid

A code for molecular dynamics simulations and various optimization schemes

jonathansemelak

Config files for my GitHub profile.

jonathansemelak.github.io

lio

Linear implementation of DFT calculations (CPU and GPU)

ml-lio

pca4namd

A bunch of python scripts to perform PCA-like methods for non adiabatic molecular dynamics.

vdos

This Python script, get_VDOS.py, is designed to calculate the Vibrational Density of States (VDOS) from molecular dynamics trajectory files. It supports different file formats and offers flexibility in terms of data processing and analysis.