Table 3.
Supplied files and their purpose.
| Folder/File | I/O | Description |
|---|---|---|
| us-x/ | ||
| equ.cpt | I | binary; checkpoint to extend a previous simulation |
| equ.gro | I | coordinates of the starting configuration |
| system.top | I | topology of the molecular system |
| martini_v2.2.itp | I | Force field and parameters |
| martini_v2.0_lipids.itp | I | Lipid force field |
| mol3.itp, mol3-2.itp | I | Solute force field |
| prod.mdp | I | simulation parameters |
| prod.tpr | I | binary; overall simulation information |
| prod.xtc | O | binary; trajectory |
| prod.edr | O | binary; various observables (e.g., energies) |
| prodx-umbrella0.xvg | O | time evolution of the solute CoMs along the z axis |
| prodf-umbrella0.xvg | O | time evolution of the pull forces along the z axis |
| pmf/ | ||
| tpr-files.dat | I | indexes paths to the tpr files |
| pullx-files.dat | I | indexes paths to the prodx files |
| bsResult.xvg | O | PMF profile with error bars |
All files provided in text format unless specified otherwise. I/O = input/output. CoM = center of mass.