<div dir="ltr"><div><div>Hello Juerg,</div><div><br></div><div>I have run SE-MD simulation with PM3 method. I run NVT calculation for 5ps. I set up the input including your suggestions and whatever mention in your paper. I again have same problem. I started with PM3 optimized structure (The initial coordinates are used from http://pubs.acs.org/doi/abs/10.1021/jz401931f ). </div><div><br></div><div> I am missing some key controls in my input. Input file and movie of trajectory are found here https://drive.google.com/folderview?id=0B56PcAs22G9NVFFkWDBtbzU1c0k&usp=sharing</div><div></div><div>.</div><div>Thank you.</div><div>Sincerely,</div><div>Bharat Sharma</div><div><br></div><div>@SET CURR_I 01</div><div><br></div><div>#@SET SEED 1000</div><div> &EXT_RESTART</div><div> RESTART_FILE_NAME ./wt_bk_PM301-1.restart</div><div> &END EXT_RESTART</div><div>#</div><div>#&EXT_RESTART</div><div># RESTART_DEFAULT TRUE</div><div># RESTART_FILE_NAME wt_bk_AM101-1.restart </div><div># RESTART_COUNTERS TRUE</div><div># RESTART_POS TRUE</div><div># RESTART_VEL TRUE</div><div># RESTART_RANDOMG TRUE</div><div>#&END EXT_RESTART</div><div><br></div><div>&GLOBAL</div><div> PROGRAM_NAME CP2K</div><div> PROJECT_NAME wt_bk_PM3${CURR_I}</div><div> RUN_TYPE MD</div><div># SEED ${SEED}</div><div> PREFERRED_FFT_LIBRARY FFTW</div><div># ECHO_INPUT YES</div><div> PRINT_LEVEL LOW</div><div> SAVE_MEM</div><div>&END GLOBAL</div><div><br></div><div>&MOTION</div><div># &PRINT</div><div># &FORCES</div><div># FORMAT XMOL</div><div># &END FORCES</div><div># &END PRINT</div><div> &MD</div><div> ENSEMBLE NVT</div><div> STEPS 10000</div><div> TIMESTEP 0.50</div><div> TEMPERATURE 300 </div><div> &THERMOSTAT</div><div> TYPE NOSE</div><div> REGION MASSIVE</div><div> &NOSE</div><div> LENGTH 3</div><div> YOSHIDA 3</div><div> TIMECON 100</div><div> MTS 2</div><div> &END NOSE</div><div> &END THERMOSTAT</div><div> &THERMAL_REGION</div><div> &PRINT</div><div> &TEMPERATURE</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END TEMPERATURE</div><div> &END PRINT</div><div> &END THERMAL_REGION</div><div> &PRINT</div><div> &ENERGY</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END ENERGY</div><div> &END PRINT</div><div> &END MD</div><div><br></div><div> &PRINT</div><div> &RESTART</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END RESTART</div><div> &RESTART_HISTORY OFF</div><div> &END RESTART_HISTORY</div><div><br></div><div> &TRAJECTORY LOW </div><div> FORMAT XYZ</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END TRAJECTORY</div><div> &VELOCITIES OFF</div><div> &END VELOCITIES</div><div> &FORCES</div><div> &END FORCES</div><div> &END PRINT</div><div>&END MOTION</div><div><br></div><div>&FORCE_EVAL</div><div> METHOD QS</div><div><br></div><div> &DFT</div><div> &SCF</div><div> SCF_GUESS ATOMIC</div><div> EPS_SCF 1.0E-7</div><div> MAX_SCF 5000</div><div> &OUTER_SCF</div><div> MAX_SCF 5000</div><div> &END OUTER_SCF</div><div> &OT T</div><div># Mingshun's scheme for PM6</div><div> PRECONDITIONER FULL_ALL</div><div> MINIMIZER DIIS</div><div> N_DIIS 9</div><div> &END OT</div><div> &PRINT</div><div> &RESTART</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END RESTART</div><div> &RESTART_HISTORY OFF</div><div> &END RESTART_HISTORY</div><div> &END PRINT</div><div> &END SCF</div><div><br></div><div> &QS</div><div> METHOD PM3</div><div># My scheme</div><div> EPS_DEFAULT 1.0E-12</div><div> EXTRAPOLATION ASPC</div><div> EXTRAPOLATION_ORDER 3</div><div> &SE</div><div># &PARAMETER</div><div># @INCLUDE PARAM</div><div># &END PARAMETER</div><div> &COULOMB</div><div> CUTOFF 12.0</div><div> RC_RANGE 0.5</div><div># RC_TAPER 2</div><div> &END COULOMB</div><div> &SCREENING</div><div> RC_RANGE 0.5</div><div> &END SCREENING</div><div> &LR_CORRECTION</div><div> CUTOFF 6.0</div><div> RC_RANGE 0.5</div><div> &END LR_CORRECTION</div><div> &EXCHANGE</div><div> CUTOFF 8.0</div><div> RC_RANGE 0.5</div><div> &END EXCHANGE</div><div> &END SE</div><div> &END QS</div><div> &MGRID</div><div> COMMENSURATE</div><div># CUTOFF 280</div><div> &END MGRID</div><div> &POISSON</div><div> POISSON_SOLVER PERIODIC</div><div> PERIODIC XYZ</div><div> &EWALD</div><div> &MULTIPOLES</div><div> MAX_MULTIPOLE_EXPANSION QUADRUPOLE</div><div> &END MULTIPOLES</div><div> EWALD_TYPE EWALD</div><div> ALPHA 0.5</div><div> GMAX 25</div><div> RCUT 6.4</div><div> &END EWALD</div><div> &END POISSON</div><div><br></div><div> &PRINT</div><div> &E_DENSITY_CUBE</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END E_DENSITY_CUBE</div><div> &END PRINT</div><div> &END DFT</div><div><br></div><div> &SUBSYS</div><div> &CELL</div><div> ABC 12.4138 12.4138 12.4138</div><div> PERIODIC XYZ </div><div> &END CELL</div><div> &COORD</div><div>----------------------------------------------</div><div>----------------------------------------------</div><div>----------------------------------------------</div><div> &END COORD</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div><br></div><div><br></div></div><div><br></div></div>