Hi, I am trying to do VLE simulations using <i>NVT</i>-GEMC
simulations in CP2K. Right now I just have one molecule type. I am confused about
the TOPOLOGY subsection.<span></span>

<p><span> </span></p>

<p>I have a system of 80 nitrogen molecules. I have three
files, 80_n2_coord.xyz (contains the coordinates of 80 N2 molecules i.e. 160 N),
80_n2_connectivity.psf (connectivity file for 80 N2 molecules), and
1_n2_connectivity.psf (connectivity file for 1 N2 molecule).<span></span></p>

<p><span> </span></p>

<p>When I use the 80 molecule connectivity file (using
following commands) : <span></span></p>

<p><span>    </span>&COORD<span></span></p>

<p><span>      </span>@INCLUDE 80_n2_coord.xyz<span></span></p>

<p><span>    </span>&END COORD<span></span></p>

<p><span>   </span>&TOPOLOGY<span></span></p>

<p><span>     
</span>CONN_FILE_FORMAT<span>       </span><span>        </span>PSF<span></span></p>

<p><span>     
</span>CONN_FILE_NAME<span>      </span><span>            </span><span> </span>80_n2_connectivity.psf<span></span></p>

<p><span>    </span>&END TOPOLOGY<span></span></p>

<p>It gives me an error:<span></span></p>

<p>Did not find MOLECULE sections for every molecule in the
simulation <span></span></p>

<p><span> </span>(make sure both input
files have all types)<span></span></p>

<p>This TOPOLOGY section worked fine for me when I did FIST <span> </span>(Force field -based) MD simulations of the
same system.<span></span></p>

<p><span> </span></p>

<p><span> </span></p>

<p>And when I use the 1 molecule connectivity file (using
following commands) :<span></span></p>

<p><span>    </span>&COORD<span></span></p>

<p><span>      </span>@INCLUDE 80_n2_coord.xyz<span></span></p>

<p><span>    </span>&END COORD<span></span></p>

<p><span>   </span>&TOPOLOGY<span></span></p>

<p><span>     
</span>CONN_FILE_FORMAT<span>       </span>MOL_SET<span></span></p>

<p><span>      </span>&MOL_SET<span></span></p>

<p><span>        </span>&MOLECULE<span></span></p>

<p><span>         
</span>CONN_FILE_NAME<span>      
</span>nitrogen_bias.psf<span></span></p>

<p><span>          </span>NMOL<span>       </span>80<span></span></p>

<p><span>        </span>&END
MOLECULE<span></span></p>

<p><span>      </span>&END MOL_SET<span></span></p>

<p><span>    </span>&END TOPOLOGY<span></span></p>

<p>It runs fine. <span> </span><span></span></p>

<p>Also, if I use 80_n2_connectivity.psf in &MOLECULE, it
gives the same error. <span></span></p>

<p><span> </span></p>

<p>I have following questions regarding this situation:<span></span></p>

<p><span> </span></p>

<p><span><span>i)<span> </span></span></span>Why CP2K does not accept the 80 molecule psf
file directly for MC simulations? Why do I need to define the &MOLECULE
section for each molecule type? And why does MD simulations run fine without
&MOLECULE section.<span></span></p>

<p><span> </span></p>

<p><span> </span></p>

<p><span><span>ii)<span>  </span></span></span>How does CP2K create the whole system from the
PSF file of just one molecule? How does it figure out the bonds between 160
atoms just from the PSF file of one molecule?<span></span></p>

<p><span> </span></p>

<p><span><span>iii)<span> </span></span></span>Is there a way to avoid defining &MOLECULE
section and providing the connectivity of the whole system using just one .psf
file?<span></span></p>

<p><span> </span></p><p><span><br></span></p><p><span>Thanks,</span></p><p><span>Ramanish<br></span></p>

<p><span> </span></p>