<div dir="ltr">Dear All <div><br></div><div>I am a beginner in CP2K and I need some help for continuing my project. </div><div>I have a small molecule which rotates and translates during the trajectory after running CP2K MD. I need to caculate the IR spectra so the rotation and translation of the molecules is unpleasant and I only need the vibrations. </div><div>I have been recommended to use the Reflective Wall in Metadynamics so that the atoms do not rotate freely. </div><div>I did not find much helpful material online to learn about these stuff (FREE ENERGY section, especially WALL REFLECTIVE, as well as the section COLVAR, TORSION). Can someone give me links to detailed explanation of how to use these sections? </div><div><br></div><div>I should also determine the atom indexes which I do not want to move (in the section COLVAR, TORSION)</div><div>which atoms should I specify while I would like the whole 2 molecules (dimer) not to rotate? </div><div><br></div><div>That would be perfect if there exist some tutorial which contains detailed explanation of these parts. </div><div>I copy my input file here, but with these specifications that I made, it did not work and the molecules still rotate and translate. </div><div><br></div><div>Thanks </div><div>Ghazaleh</div><div><br></div><div><div>&GLOBAL</div><div>PROJECT_NAME thion_dimer-dft-MD</div><div>RUN_TYPE MD</div><div>PRINT_LEVEL LOW</div><div>&END GLOBAL</div><div>#-----------------------------------------------------------------------------------------------------------------------------------------------------------</div><div>&FORCE_EVAL</div><div>&DFT</div><div>BASIS_SET_FILE_NAME GTH_BASIS_SETS</div><div>POTENTIAL_FILE_NAME GTH_POTENTIALS</div><div> &MGRID</div><div> CUTOFF 500</div><div> REL_CUTOFF 30</div><div> NGRIDS 4</div><div> &END MGRID</div><div> &SCF</div><div> SCF_GUESS ATOMIC</div><div> MAX_SCF 300</div><div> &OT</div><div> MINIMIZER DIIS</div><div> PRECONDITIONER FULL_SINGLE_INVERSE</div><div> &END OT</div><div> &PRINT</div><div> &RESTART</div><div> &EACH</div><div> MD 2000</div><div> &END EACH</div><div> &END RESTART</div><div> &END PRINT</div><div> &END SCF</div><div> &LOCALIZE</div><div> METHOD CRAZY</div><div> MAX_ITER 2000</div><div> &PRINT</div><div> &WANNIER_CENTERS</div><div> IONS+CENTERS</div><div> FILENAME =thion_dimer-dft-MD-wc.xyz</div><div> &EACH</div><div> MD 5</div><div> &END EACH</div><div> &END WANNIER_CENTERS</div><div> &END PRINT</div><div> &END LOCALIZE</div><div> &XC</div><div> &XC_FUNCTIONAL BLYP</div><div> &END XC_FUNCTIONAL</div><div> &XC_GRID</div><div> XC_DERIV NN10_SMOOTH</div><div> XC_SMOOTH_RHO NN10</div><div> &END XC_GRID</div><div> &VDW_POTENTIAL</div><div> POTENTIAL_TYPE PAIR_POTENTIAL</div><div> &PAIR_POTENTIAL</div><div> TYPE DFTD3</div><div> PARAMETER_FILE_NAME dftd3.dat</div><div> REFERENCE_FUNCTIONAL BLYP</div><div> &END PAIR_POTENTIAL</div><div> &END VDW_POTENTIAL</div></div><div><div> &END XC</div><div>&PRINT</div><div> &MOMENTS</div><div> PERIODIC FALSE</div><div> &EACH</div><div> MD 1</div><div> &END</div><div> MAX_MOMENT 1</div><div> FILENAME =dipole-thion_dimer-dft-MD.traj</div><div> &END MOMENTS</div><div> &END</div><div>&END DFT</div><div>#---------------------------------------------------------------------------------------------------------------------------------------------------------</div><div>&SUBSYS</div><div> &CELL</div><div> ABC 28 28 28</div><div> ALPHA_BETA_GAMMA 90.00 90.00 90.00</div><div> PERIODIC XYZ ! => Periodicity of the system</div><div> &END CELL</div><div> &TOPOLOGY</div><div> COORD_FILE_NAME min-thion_dimer-lf.xyz</div><div> COORD_FILE_FORMAT xyz</div><div> &END TOPOLOGY</div><div>&KIND O</div><div> BASIS_SET DZVP-GTH</div><div> POTENTIAL GTH-BLYP-q6</div><div> &END KIND</div><div>&KIND C</div><div> BASIS_SET DZVP-GTH</div><div> POTENTIAL GTH-BLYP-q4</div><div> &END KIND</div><div>&KIND N</div><div> BASIS_SET DZVP-GTH</div><div> POTENTIAL GTH-BLYP-q5</div><div> &END KIND</div><div>!&KIND D</div><div>! BASIS_SET DZVP-GTH</div><div>! POTENTIAL GTH-BLYP-q1</div><div>! MASS 2.0</div><div>! ELEMENT H</div><div>! &END KIND</div><div>&KIND H</div><div> BASIS_SET DZVP-GTH</div><div> POTENTIAL GTH-BLYP-q1</div><div> &END KIND</div><div>&KIND S</div><div> BASIS_SET DZVP-GTH</div><div> POTENTIAL GTH-BLYP-q6</div><div> &END KIND</div><div>&COLVAR</div><div> &TORSION</div><div> ATOMS 1 3 8 9</div><div> &END TORSION</div><div> &END COLVAR</div><div>&END SUBSYS</div><div>&END FORCE_EVAL</div></div><div><div>#--------------------------------------------------------------------------------------------------------------------------------------------------------</div><div>&MOTION</div><div> &MD</div><div> ENSEMBLE NVT</div><div> STEPS 20000</div><div> TIMESTEP 0.5</div><div> TEMPERATURE 300.0</div><div> COMVEL_TOL 1e-8</div><div> ANGVEL_ZERO T</div><div> ANGVEL_TOL 1e-12</div><div> &THERMOSTAT</div><div> TYPE NOSE</div><div> &NOSE</div><div> TIMECON 100</div><div> &END NOSE</div><div> &END THERMOSTAT</div><div> &END MD</div><div>&FREE_ENERGY</div><div> METHOD METADYN</div><div> &METADYN</div><div> MIN_DISP -1.0000000000000000E+00</div><div> OLD_HILL_NUMBER 0</div><div> OLD_HILL_STEP 0</div><div> NHILLS_START_VAL 0</div><div> &METAVAR</div><div> SCALE 1.0000000000000000E+00</div><div> COLVAR 1</div><div> &WALL</div><div> TYPE REFLECTIVE</div><div> POSITION -1.5707963267948966E+00</div><div> &REFLECTIVE</div><div> DIRECTION WALL_MINUS</div><div> &END REFLECTIVE</div><div> &END WALL</div><div> &WALL</div><div> TYPE REFLECTIVE</div><div> POSITION 1.5707963267948966E+00</div><div> &REFLECTIVE</div><div> DIRECTION WALL_PLUS</div><div> &END REFLECTIVE</div><div> &END WALL</div><div> &END METAVAR</div><div> &PRINT</div><div> &PROGRAM_RUN_INFO OFF</div><div> &END PROGRAM_RUN_INFO</div><div> &COLVAR OFF</div><div> &END COLVAR</div><div> &END PRINT</div><div> &END METADYN</div><div> &END FREE_ENERGY</div><div> &PRINT</div><div> &RESTART</div><div> &EACH</div><div> MD 20</div><div> &END EACH</div></div><div><div> &END RESTART</div><div>&TRAJECTORY</div><div>FILENAME thion_dimer-dft-trj.xyz</div><div>FORMAT XYZ</div><div>&EACH</div><div>MD 1</div><div>&END EACH</div><div>&END TRAJECTORY</div><div>&VELOCITIES</div><div>LOG_PRINT_KEY T</div><div>FORMAT XYZ</div><div>&EACH</div><div>MD 1</div><div>&END EACH</div><div>ADD_LAST NUMERIC</div><div>&END VELOCITIES</div><div> &END PRINT</div><div>&END MOTION</div><div>#-------------------------------------------------------------------------------------------------------------------------------------</div><div>!&EXT_RESTART</div><div>!RESTART_DEFAULT F</div><div>!RESTART_FILE_NAME min-thion_dimer-1.restart</div><div>!RESTART_POS T</div><div>!RESTART_VEL T</div><div>!RESTART_THERMOSTAT T</div><div>!&END EXT_RESTART</div></div><div><br></div></div>