06_HTMD_Tunnels: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites

# Contains input, output and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Tunnels schemes. 

# The folders are organized as:

Input_files/ # Contains .parm7 and .rst files of 30 seed conformations obtained from equilibrations and used for adaptive sampling inputs, run_adaptiveMD.py : Script file executing the adaptive sampling using distance matrix considering protein C-alpha atoms and heavy atoms of DBE.
rep1/
└── adaptive_data/
    ├── generators/ # Contains the initial generator files provided by the user
    │   ├── ../structure.parm7
    │   ├── ../input.ncrst
    │   └── ...
    ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated)
    │   ├── ../equil1.log
    │   ├── ../input.ncrst
    │   └── ...
└──rep2/
...
...