04_HTMD_Cavity: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites

<p># Contains input, output and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Cavity schemes.&nbsp;</p> <p># The forders are organized as:</p> <p>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.<br>rep1/<br>└── adaptive_data/<br>&nbsp; &nbsp; ├── generators/ # Contains the initial generator files provided by the user<br>&nbsp; &nbsp; │ &nbsp; ├── ../structure.parm7<br>&nbsp; &nbsp; │ &nbsp; ├── ../input.ncrst<br>&nbsp; &nbsp; │ &nbsp; └── ...<br>&nbsp; &nbsp; ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated)<br>&nbsp; &nbsp; │ &nbsp; ├── ../equil1.log<br>&nbsp; &nbsp; │ &nbsp; ├── ../input.ncrst<br>&nbsp; &nbsp; │ &nbsp; └── ...<br>└──rep2/<br>...<br>...<br>&nbsp;</p>