askusay

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_tutorial

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

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

askusay/Altmetrics_parser

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

askusay/AMBER-Maestro-lipid-tutorial

Tutorial to build AMBER compatable protein+lipid systems

askusay/cg2at

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

askusay/CHARMM-GUI_GROMOS_conversion_tutorial

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

askusay/Desmond_cms_converter

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

askusay/gro_to_desmond

A basic converter from the gromacs topology format to desmond CMS

askusay/martinize.py

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

askusay/MD_box_fixer

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

askusay/OpenMM_alchemy_scripts

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

askusay/OpenMM_force_scripts

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

askusay/OpenMM_misc_scripts_notebooks

Some useful OpenMM scripts

askusay/ParmEd

Parameter/topology editor and molecular simulator

askusay/pbc_mindist

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

askusay/qligfep

askusay/TTClust

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

askusay/UA_to_AA_converter

askusay/Visualise_martini_bond_network