# NAMD-MD

**Repository Path**: hhtcadd/NAMD-MD

## Basic Information

- **Project Name**: NAMD-MD
- **Description**: Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 2
- **Created**: 2022-01-11
- **Last Updated**: 2022-07-11

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# NAMD-MD
This repository try to introduce molecular dynamics of protein-ligand complex to more people, especially those beginners, with all open-souuced resouces. VMD (https://www.ks.uiuc.edu/), NAMD (https://www.ks.uiuc.edu/) and py3Dmol (https://github.com/avirshup/py3dmol), as well as open babel (https://github.com/openbabel/openbabel) are the main components contained in this protocal. The force file package used is charmm as per https://www.charmm.org/charmm/resources/charmm-force-fields/ for protein, small moleucles are paramerized by web server LigPargen (http://zarbi.chem.yale.edu/ligpargen/).

This is designed only for learning purpose, anyone with commercial purpose might need to check out by themself if they need a commercial license in relation to some certain package, even these are all "open source".

# Usage
It is assumed you already got anaconda installed on your linux computer, visit https://docs.anaconda.com/# to get one if not installed.
```
git clone https://github.com/quantaosun/NAMD-MD
```
```
cd NAMD-MD
```
Create a new Conda environment named "NAMD-MD"
```
conda create -n NAMD-MD python=3.7
```
Activate the new environment 
```
conda activate NAMD-MD
```
In the new environment, install jupyter notebook
```
conda install jupyter
```
Start jupyter notebook and run the "NAMD-MD_local.ipynb"
```
jupyter notebook NAMD-MD_local.ipynb
```

# If you have problem opening jupyter notebook in your "NAMD-MD" environment, try 
```
conda remove jupyter
```
```
sudo apt install jupyter
```
```
jupyter notebook
```

The NAMD-MD.ipynb include how to set up a general solution MD, proteins with membrane also discussed, it was designed use on Colab.
The NAMD-MD_local.opynb is a consised version only for a soution system without membrane, designed to use on local linux system.