| _version_ | 1866901922071445504 |
|---|---|
| author | Hartojo, Alfred Doyle, Matthew |
| author_facet | Hartojo, Alfred Doyle, Matthew |
| contents | <p dir="auto">Welcome! Files pertaining to the MD simulations conducted for the "First inhibitor of a bacterial two-partner secretion system" paper are deposited here:</p> <p dir="auto">Contents:</p> <ul> <li>POTRA1-P1∆Nt (Used in Fig. 4f and S9) </li> </ul> <p dir="auto">All simulations are conducted (n = 3). Each folder contains files used for input or output (in .zip format).</p> <p dir="auto">Used for all 3 Replicates per system</p> <ul> <li>Initial AlphaFold2 Predicted Structure (.pdb)</li> <li>Cleaned Initial Structure (.pdb)</li> </ul> <p dir="auto">Processed separately per replicate</p> <ul> <li>GROMACS Initial Setup Files (.gro,.itp)</li> <li>GROMACS Structure Configuration Files (.gro)</li> <li>GROMACS Solvation Setup Files (.gro,.top)</li> <li>GROMACS Energy Minimisation Files (.gro,.edr)</li> <li>GROMACS NVT Equilibration Files (.gro,.cpt)</li> <li>GROMACS NPT (with constraint) Equilibrium Files (.gro,.cpt)</li> <li>GROMACS NPT (without constraint) Equilibration Files (.gro,.cpt)</li> <li>GROMACS Production Structure, Trajectory, and Other Files (.gro,.pdb,.trr,.xtc,.edr,tpr)</li> <li>GROMACS PBC Fixed Trajectories (in the order below)</li> </ul> <p>-pbc -whole -ur compact tric -> -pbc -nojump -ur compact -tric -> <strong>-pbc -mol -ur compact -centre tric</strong></p> <p>[<strong>Trajectory used for final analysis</strong>]</p> <ul> <li>And logs corresponding to each setup (.txt).</li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18640231 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | MD Files for "First inhibitor of a bacterial two-partner secretion system" [POTRA1-P1∆Nt; n = 3] Hartojo, Alfred Doyle, Matthew <p dir="auto">Welcome! Files pertaining to the MD simulations conducted for the "First inhibitor of a bacterial two-partner secretion system" paper are deposited here:</p> <p dir="auto">Contents:</p> <ul> <li>POTRA1-P1∆Nt (Used in Fig. 4f and S9) </li> </ul> <p dir="auto">All simulations are conducted (n = 3). Each folder contains files used for input or output (in .zip format).</p> <p dir="auto">Used for all 3 Replicates per system</p> <ul> <li>Initial AlphaFold2 Predicted Structure (.pdb)</li> <li>Cleaned Initial Structure (.pdb)</li> </ul> <p dir="auto">Processed separately per replicate</p> <ul> <li>GROMACS Initial Setup Files (.gro,.itp)</li> <li>GROMACS Structure Configuration Files (.gro)</li> <li>GROMACS Solvation Setup Files (.gro,.top)</li> <li>GROMACS Energy Minimisation Files (.gro,.edr)</li> <li>GROMACS NVT Equilibration Files (.gro,.cpt)</li> <li>GROMACS NPT (with constraint) Equilibrium Files (.gro,.cpt)</li> <li>GROMACS NPT (without constraint) Equilibration Files (.gro,.cpt)</li> <li>GROMACS Production Structure, Trajectory, and Other Files (.gro,.pdb,.trr,.xtc,.edr,tpr)</li> <li>GROMACS PBC Fixed Trajectories (in the order below)</li> </ul> <p>-pbc -whole -ur compact tric -> -pbc -nojump -ur compact -tric -> <strong>-pbc -mol -ur compact -centre tric</strong></p> <p>[<strong>Trajectory used for final analysis</strong>]</p> <ul> <li>And logs corresponding to each setup (.txt).</li> </ul> |
| title | MD Files for "First inhibitor of a bacterial two-partner secretion system" [POTRA1-P1∆Nt; n = 3] |
| url | https://doi.org/10.5281/zenodo.18640231 |