<div dir="ltr">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 </div>