riazi-r Goto Github PK

abf

Absolute Binding Free Energy originally developed by Quantaosun

apbs

Software for biomolecular electrostatics and solvation calculations

archer2-advanced-use-of-lammps

Repo for Advanced Use of LAMMPS course

automapper

A package of tools for automating the file preparation for the LAMMPS fix bond/react.

awesomethermodynamics

A curated list of awesome resources on Thermodynamics

cheminformatics-teaching-material

Resources, Code, and Other things I use to teach Cheminformatics.

course-md

ensemble_md

A python package for performing GROMACS simulation ensembles

fep-minus

Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus identical calculation but for FREE (Only for Academic community). Give it a like if this helps you so that I know this is useful to others.

fftw3

DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)

fluxionalize

An open source conformational search method.

gmx-2023-colab

Gromacs scrpits, mdp and commands refrences

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

ibm3202

Google Colab Tutorials for IBM3202

kimmdy

reactive MD python pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)

lammps

lammps inputs and scripts

lammps_google-colab

Using LAMMPS Package for Molecular Dynamics and running by using Google Colab

lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs

making-it-rain

Cloud-based molecular simulations for everyone

moleculardynamics-render-

MD analysis/setup scripts

namd-mmpbgbsa

This script to running NAMD Molecular Dynamics in Google Colab, and free energy calculation using Linear Interaction Energy (LIE), MMPBSA and MMGBSA

namd-rest

REST Implementation in NAMD

namd_to_charmm-gui

Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

namdnotebooks

Jupyter Notebooks for Molecular Dynamics

nmr2gmxpy

Read NMR data files for proteins and generate GROMACS input files

pmftoolbox

A Qt GUI Toolbox for post-processing the potentail of mean force (PMF)

pytherm-applied-thermodynamics

Educational ipython source code for applied thermodynamics.

remd-temperature-generator

Temperature generator for Replica Exchange MD simulations

remd_analysis

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

riazi-r

Config files for my GitHub profile.