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/......