I found the problem in the MM_INDEX of the link atoms. Now it works. <div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, September 6, 2022 at 12:35:40 AM UTC+2 Sayyed Jalil Mahdizadeh wrote: </div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hello,<div>I'm running QMMM MD simulation but got the following error message.</div><div>Can someone help me with this issue?</div><div> </div><div>"A non-periodic calculation has been requested but the system size </div><div>exceeds the cell size in at least one of the non-periodic" </div><div> </div><div>Here is my input file:</div><div> </div><div>&GLOBAL PROJECT METADYN PRINT_LEVEL LOW RUN_TYPE MD &END GLOBAL &FORCE_EVAL METHOD QMMM STRESS_TENSOR ANALYTICAL &DFT CHARGE 0 MULTIPLICITY 1 &QS METHOD GPW &END QS &POISSON PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics PSOLVER PERIODIC #The way to solve Poisson equation &END POISSON &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3(BJ) PARAMETER_FILE_NAME ./dftd3.dat REFERENCE_FUNCTIONAL PBE CALCULATE_C9_TERM .TRUE. R_CUTOFF [angstrom] 10.0 &END PAIR_POTENTIAL &END VDW_POTENTIAL &END XC &MGRID COMMENSURATE CUTOFF 300 REL_CUTOFF 40 &END MGRID &SCF MAX_SCF 30 EPS_SCF 1.0E-6 SCF_GUESS ATOMIC &OT MINIMIZER DIIS PRECONDITIONER FULL_SINGLE_INVERSE &END &OUTER_SCF EPS_SCF 1.0E-6 MAX_SCF 10 &END &PRINT &RESTART OFF &END &RESTART_HISTORY OFF &END &END &END SCF BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS WFN_RESTART_FILE_NAME WFN-RESTART.wfn &END DFT &MM &FORCEFIELD PARMTYPE AMBER PARM_FILE_NAME protein_LJ_mod.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] 114.2123865514 114.2126337318 114.<a href="tel:(361)%20672-1715" value="+13616721715" target="_blank" rel="nofollow">3616721715</a> ALPHA_BETA_GAMMA 90 90 90 &END CELL &TOPOLOGY CONN_FILE_FORMAT AMBER CONN_FILE_NAME protein_LJ_mod.prmtop &END TOPOLOGY &KIND C ELEMENT C BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND H ELEMENT H BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND N ELEMENT N BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q5 &END KIND &KIND O ELEMENT O BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND P ELEMENT P BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q5 &END KIND &KIND NA+ ELEMENT Na &END KIND &KIND Cl- ELEMENT Cl &END KIND &END SUBSYS &QMMM ECOUPL GAUSS USE_GEEP_LIB 6 &CELL ABC 20 20 20 ALPHA_BETA_GAMMA 90 90 90 &END CELL &QM_KIND O MM_INDEX 5630 5627 5621 5595 5596 5205 5206 5346 &END QM_KIND &QM_KIND C MM_INDEX 5583 5584 5585 5586 5588 5589 5590 5591 5592 5593 5594 5615 5626 5620 5619 5622 5201 5204 5337 5340 5341 5343 5345 5348 5350 &END QM_KIND &QM_KIND H MM_INDEX 5640 5641 5638 5639 5636 5637 5634 5635 5633 5632 5631 5628 5623 5624 5625 5629 5616 5617 5618 5203 5202 5207 5338 5339 5342 5344 5347 5349 5351 &END QM_KIND &QM_KIND N MM_INDEX 5587 &END QM_KIND &LINK MM_INDEX 6582 QM_INDEX 6583 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 5597 QM_INDEX 5593 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 5199 QM_INDEX 5201 LINK_TYPE IMOMM &END LINK &LINK MM_INDEX 5335 QM_INDEX 5337 LINK_TYPE IMOMM &END LINK &END QMMM &END FORCE_EVAL &MOTION &MD ENSEMBLE NVT TIMESTEP [fs] 0.5 STEPS 2000000 TEMPERATURE 298 &THERMOSTAT TYPE NOSE REGION GLOBAL &NOSE TIMECON [fs] 100. &END NOSE &END THERMOSTAT &END MD &FREE_ENERGY METHOD METADYN &METADYN USE_PLUMED .TRUE. PLUMED_INPUT_FILE ./<a href="http://plumed.in" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://plumed.in&source=gmail&ust=1662552274450000&usg=AOvVaw32CvYUTvGjjP-8w43g07Gx">plumed.in</a> &END METADYN &END FREE_ENERGY &PRINT &RESTART &EACH MD 100 &END &END &RESTART_HISTORY &EACH MD 100 &END &END &TRAJECTORY FORMAT DCD &EACH MD 20 &END &END &END PRINT &END MOTION &EXT_RESTART RESTART_FILE_NAME NPT-1.restart RESTART_COUNTERS .FALSE. RESTART_THERMOSTAT .FALSE. &END </div></blockquote></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/1cb268dd-2661-4f82-a2d3-53c210fdbfd0n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/1cb268dd-2661-4f82-a2d3-53c210fdbfd0n%40googlegroups.com</a>.