PARA_RES OFF.

[liuxians... at gmail.com]

Hi cp2k developers/users,

Example tests/Fist/sample_cp2k/UO2-2x2x2-coord-2.xyz shown below: Are all 
atoms of molecule type UO2? How I can I define separate molecules to do MM. 

   U       0.000000    0.000000    0.000000  UO2
   U      0.000000    2.723735    2.723735  UO2
   U      2.723735    0.000000    2.723735  UO2
   U      2.723735    2.723735    0.000000  UO2
   O      1.361868    1.361868    1.361868  UO2
   O      1.361868    1.361868    4.085602  UO2
   O      1.361868    4.085602    1.361868  UO2
   O      4.085602    1.361868    1.361868  UO2
   O      1.361868    4.085602    4.085602  UO2
   O      4.085602    1.361868    4.085602  UO2
------------------------------------cut----------------------------


In example tests/Fist/sample_cp2k/UO2-2x2x2-coord-1.xyz  shown below: Are 
there two molecules of 1 and 2 of type UO2 ?. "UO2 1" defines first 
molecule, "UO2 2" defines second molecule?
   U      0.000000    0.000000    0.000000  UO2  1
   U      0.000000    2.723735    2.723735  UO2  1
   U      2.723735    0.000000    2.723735  UO2  1
   U      2.723735    2.723735    0.000000  UO2  1
   O      1.361868    1.361868    1.361868  UO2  1
   O      1.361868    1.361868    4.085602  UO2  1
   O      1.361868    4.085602    1.361868  UO2  1
   O      4.085602    1.361868    1.361868  UO2  1
   O      1.361868    4.085602    4.085602  UO2  1
   O      4.085602    1.361868    4.085602  UO2  1
   O      4.085602    4.085602    1.361868  UO2  1
   O      4.085602    4.085602    4.085602  UO2  1
   U      0.000000    0.000000    5.447470  UO2  2
   U      0.000000    2.723735    8.171205  UO2  2
   U      2.723735    0.000000    8.171205  UO2  2
   U      2.723735    2.723735    5.447470  UO2  2
   O      1.361868    1.361868    6.809337  UO2  2
   O      1.361868    1.361868    9.533072  UO2  2
   O      1.361868    4.085602    6.809337  UO2  2
   O      4.085602    1.361868    6.809337  UO2  2
   O      1.361868    4.085602    9.533072  UO2  2
   O      4.085602    1.361868    9.533072  UO2  2
   O      4.085602    4.085602    6.809337  UO2  2
   O      4.085602    4.085602    9.533072  UO2  2
------------------------------------cut----------------------------

But I have no protein but Sio2 surface with benzene solvent , Can I ignore 
residue column? How can I define separate molecules to do a FIST MM 
simulation to apply electrostatic and LJ interactions. What happens when 
PARA_RES is OFF and ON. 

If PARA_RES ON: 6th column's 1, 2, 3.... acts as separate molecules?
If PARA_RES OFF: 5th column's 1, 2, 3 .,.,. acts as separate molecules?

CONN_FILE_FORMAT:  USER  Allows the definition of molecules and residues 
based on the 5th and 6th column of the COORD section. This option can be 
handy for the definition of molecules with QS or to save memory in the case 
of very large systems (use PARA_RES off).

PARA_RES For a protein, each residue is now considered a molecule.


 Help!!

Regards,
Liu
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