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altmetrics_parser

Uses PyAlmetric to get almetric info over command line or processes csv file with multiple article DOIs

amber-maestro-lipid-tutorial

Tutorial to build AMBER compatable protein+lipid systems

cg2at

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)

charmm-gui_gromos_conversion

Instructions and script for converting systems generating from CHARMM-GUI to the GROMOS united atom format

desmond_cms_converter

Converts .cms to .pdb using PyMOL and renames residues/atoms to facilitate parameterisation using AMBER/CHARMM

gro_to_desmond

A basic converter from the gromacs topology format to desmond CMS

martinize.py

Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.

md_box_fixer

Fixes the issue of proteins not being centred in the simulation box

molecular-illustrations

A collection of illustrations based on published and soon to be published work

openmm_alchemy_scripts

Example note-books for trying out simulations with various alchemical states

openmm_force_scripts

This repository contains OpenMM custom forces written as functions for ease of use

openmm_misc_scripts_notebooks

Some useful OpenMM scripts

parmed

Parameter/topology editor and molecular simulator

pbc_mindist

Python code to calculate distances between periodic images in molecular dynamics simulations.

qligfep

raymo111

My awesome profile README

tqdm

A Fast, Extensible Progress Bar for Python and CLI

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

ua_to_aa_converter

visualise_martini_bond_network