Dear All I am trying to use REFTRAJ to calculate force and energy from trajectory file. <div> </div><div>&GLOBAL PROJECT MD PRINT_LEVEL LOW RUN_TYPE MD &END GLOBAL &FORCE_EVAL METHOD QMMM STRESS_TENSOR ANALYTICAL &DFT &LS_SCF EXTRAPOLATION_ORDER 3 &END LS_SCF BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME POTENTIAL &MGRID CUTOFF 280 REL_CUTOFF 40 NGRIDS 5 &END MGRID &QS EPS_DEFAULT 1.0E-6 EXTRAPOLATION_ORDER 3 &END QS &SCF SCF_GUESS ATOMIC &OT ON MINIMIZER DIIS &END OT EPS_SCF 1.0E-6 &PRINT &RESTART OFF &END &END &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &vdW_POTENTIAL DISPERSION_FUNCTIONAL PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3(BJ) PARAMETER_FILE_NAME dftd3.dat REFERENCE_FUNCTIONAL PBE &END PAIR_POTENTIAL &END vdW_POTENTIAL &END XC &END DFT &MM &FORCEFIELD PARMTYPE AMBER PARM_FILE_NAME System.prmtop &SPLINE EMAX_SPLINE 1.0E8 RCUT_NB [angstrom] 10 &END SPLINE &END FORCEFIELD &POISSON &EWALD EWALD_TYPE SPME ALPHA .40 GMAX 80 &END EWALD &END POISSON &END MM &SUBSYS &CELL ABC [angstrom] 58.9710000 58.6940000 57.5120000 ALPHA_BETA_GAMMA 90 90 90 &END CELL &TOPOLOGY CONN_FILE_FORMAT AMBER CONN_FILE_NAME System.prmtop COORD_FILE_FORMAT CRD COORD_FILE_NAME System.inpcrd &END TOPOLOGY &KIND H ELEMENT H BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND C ELEMENT C BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND O ELEMENT O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND F ELEMENT F BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q7 &END KIND &END SUBSYS &QMMM ECOUPL NONE !USE_GEEP_LIB 5 CENTER EVERY_STEP &CELL ABC 30 30 30 ALPHA_BETA_GAMMA 90 90 90 &END CELL &QM_KIND O MM_INDEX 64 471 59 46 334 347 468 41 329 352 437 441 451 457 466 &END QM_KIND &QM_KIND H MM_INDEX 57 65 60 54 51 53 52 47 39 42 330 327 335 342 339 341 340 345 353 348 472 473 469 470 434 435 436 439 443 444 445 446 448 450 453 455 456 459 460 461 463 464 465 467 &END QM_KIND &QM_KIND C MM_INDEX 66 63 61 58 55 56 49 50 48 45 43 40 37 38 325 326 336 333 331 328 337 338 343 346 344 354 351 349 433 438 440 442 447 449 452 454 458 462 &END QM_KIND &QM_KIND F MM_INDEX 62 44 332 350 &END QM_KIND &LINK MM_INDEX 67 QM_INDEX 66 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 31 QM_INDEX 37 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 355 QM_INDEX 354 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 319 QM_INDEX 325 LINK_TYPE IMOMM &END LINK &END QMMM &END FORCE_EVAL &MOTION </div><div> &MD ENSEMBLE REFTRAJ &REFTRAJ EVAL_ENERGY_FORCES T EVAL_FORCES T TRAJ_FILE_NAME traj_till3n.xyz FIRST_SNAPSHOT 1 LAST_SNAPSHOT 1993 STRIDE 1 &END REFTRAJ &END MD &END MOTION But its not working with the following error *** WARNING in qmmm_util.F:190 :: One or few QM atoms are within the SKIN *** *** of the quantum box. Check your run and you may possibly consider: the *** *** activation of the QMMM WALLS around the QM box, switching ON the *** *** centering of the QM box or increase the size of the QM cell. CP2K *** *** CONTINUE but results could be meaningless. *** I am not sure why is it not centering the qm part in the given box. Because I use the same qm settings to run a MD with level of theory and it works. But during reftraj its not centering the qm part and which maybe creating the problem. Any suggestion will be really helpful. Thank you. Kind regards Chintu</div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>. To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/81c4ec8c-0110-497e-9593-15bed2505940n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/81c4ec8c-0110-497e-9593-15bed2505940n%40googlegroups.com</a>.