<div dir="ltr"><p class="separator" style="text-align: center; clear: both;"><a imageanchor="1" href="https://lh3.googleusercontent.com/-5PbrHXi3hmo/WjfyO3bqihI/AAAAAAAADfY/L_BMOS3Jnow6RiaqKE4xX-nxo5lNioELQCLcBGAs/s1600/ddd.png" style="margin-left: 1em; margin-right: 1em;"><img src="https://lh3.googleusercontent.com/-5PbrHXi3hmo/WjfyO3bqihI/AAAAAAAADfY/L_BMOS3Jnow6RiaqKE4xX-nxo5lNioELQCLcBGAs/s320/ddd.png" border="0" width="320" height="292"></a><a imageanchor="1" href="https://lh3.googleusercontent.com/-QXmkg9wMY3c/WjfyHaLaalI/AAAAAAAADfQ/nAEiKbekjwcsM83nZed4-hRoHioMORGTQCLcBGAs/s1600/cp2k11.png" style="margin-left: 1em; margin-right: 1em;"><img src="https://lh3.googleusercontent.com/-QXmkg9wMY3c/WjfyHaLaalI/AAAAAAAADfQ/nAEiKbekjwcsM83nZed4-hRoHioMORGTQCLcBGAs/s320/cp2k11.png" border="0" width="320" height="301"></a><br></p><div><br></div><div><br></div><div>Hi CP2K group,</div><div><br></div>I am trying to create a PSF file for ALOOH surface. I have a particular requirement that the psf file should have connections shown as in left figure.<div><br></div><div>I have created the PSF file, but CP2K shows error: </div><div>CP2K requires molecules to be contiguous and we have detected a non *                                                                                                                               <div> * [ABORT]    contiguous one!! In particular a molecule defined from index (   *                                                                                                                               </div><div> *  \___/  1) to (   210) contains other molecules, not connected! </div><div><br></div><div><br></div><div>My PSF file look like this: </div><div><br></div><div><div>     256 !NATOM                                                                                                                                                                                                </div><div>       1 14   01   DIAS Al1  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       2 14   01   DIAS Al2  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       3 03   01   DIAS Al3  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       4 03   01   DIAS Al4  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       5 13   01   DIAS Al5  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       6 13   01   DIAS Al6  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       7 02   01   DIAS Al7  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       8 02   01   DIAS Al8  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       9 12   01   DIAS Al9  YA     0.000000        0.0000           0                                                                                                                                         </div><div>      10 12   01   DIAS Al1A YA     0.000000        0.0000           0                                                                                                                                         </div><div>      11 01   01   DIAS Al1B YA     0.000000        0.0000           0 </div></div><div><br></div><div>Questions:</div><div>1) If it is same molecule, then in PSF file should SEGMENT ID should be defined exactly in a row? for instance</div><div><br></div><div>which format is correct for CP2K. See SEGMENT ID (second column).. Should each molecule be defined in a row or it can be expressed randomly?</div><div><br></div><div><div> 256 !NATOM                                                                                                                                                                                                </div><div>       1 AA   01   DIAS Al1  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       2 BB  01   DIAS Al4  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       3 AA  01   DIAS Al3  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       4 AA 01   DIAS Al2  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       5 BB  01   DIAS Al5  YA     0.000000        0.0000           0      </div></div><div><br></div><div><br></div><div><div> 256 !NATOM                                                                                                                                                                                                </div><div>       1 AA   01   DIAS Al1  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       2 AA  01   DIAS Al2  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       3 AA  01   DIAS Al3  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       4 BB  01   DIAS Al4  YA     0.000000        0.0000           0                                                                                                                                         </div><div>       5 BB  01   DIAS Al5  YA     0.000000        0.0000           0      </div></div><div><br></div><div> </div><div>2) In my current ALO(OH), except for the non-hydroxy oxygen everything are connected. I could create PSF connecting all atoms (easier to create for me compared to the PSF separating the non-hydroxy oxygen). Is there any easier way to define non-hydroxy oxygens as separate molecules, so that I can have 1-3 VdW, EI.</div><div><br></div><div><br></div><div>Please let me know. Attached are my PSF, input and PDB files.</div></div></div>