<div dir="ltr"><div>To add an observation, if I select only the organic molecule (in quantum description) and exclude the QM water molecules in my QM/MM md run then it is running fine. </div>Any suggestion? <div class="gmail_extra"> <div class="gmail_quote">On Fri, Mar 14, 2014 at 11:08 AM, tarak karmakar <<a href="mailto:tarak...@gmail.com" target="_blank">tarak...@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div dir="ltr"><div><div><div><div><div>Dear All, </div>I'm trying to perform a QM/MM simulation in CP2K by taking the well equilibrated (seeing the tot_eng, pot_eng, temperature) configuration obtained from classical simulation in NAMD with charmm force field. </div> </div>In QM/MM input file I use the simulation box lengths and its center of mass from the .xst file (NAMD) for a selected frame. The QM/MM input file is given below. &FORCE_EVAL METHOD QMMM #.................................................. &DFT CHARGE -3 ROKS BASIS_SET_FILE_NAME GTH_BASIS_SETS POTENTIAL_FILE_NAME GTH_POTENTIALS &MGRID CUTOFF 280 COMMENSURATE &END MGRID &SCF ## Max iterations and convergence limit for minimization SCF_GUESS ATOMIC ##atomic,restart,random,or core EPS_SCF 1.0e-6 MAX_SCF 250 &OUTER_SCF MAX_SCF 10 &END OUTER_SCF &OT ON PRECOND_SOLVER INVERSE_CHOLESKY PRECONDITIONER FULL_KINETIC MINIMIZER CG ROTATION .TRUE. &END OT &END SCF &QS EPS_DEFAULT 1.0E-10 MAP_CONSISTENT EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 3 &END QS &XC &XC_GRID XC_SMOOTH_RHO NN10 XC_DERIV SPLINE2_SMOOTH &END XC_GRID &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &END XC &POISSON POISSON_SOLVER MULTIPOLE PERIODIC NONE &END POISSON &END DFT #..................................................... &MM &FORCEFIELD parm_file_name ./omp_new_parm.pot parmtype CHM EI_SCALE14 1.0 &SPLINE EMAX_SPLINE 1.0E8 RCUT_NB 12.0 &END &END FORCEFIELD &POISSON &EWALD EWALD_TYPE spme ALPHA .5 GMAX 80 80 80 O_SPLINE 6 &END EWALD &END POISSON &PRINT &FF_INFO &END FF_INFO &END PRINT &END MM #.......................................................... &QMMM E_COUPL GAUSS USE_GEEP_LIB 7 &WALLS TYPE REFLECTIVE WALL_SKIN 0.5 0.5 0.5 &END WALLS &CELL ABC [angstrom] 20.0 20.0 20.0 PERIODIC XYZ &END CELL &PERIODIC GMAX 0.11 &MULTIPOLE EWALD_PRECISION 0.000001 RCUT 11.0 ANALYTICAL_GTERM &END MULTIPOLE &END PERIODIC &INTERPOLATOR EPS_R 1.0e-14 EPS_X 1.0e-14 MAXITER 150 &END INTERPOLATOR &QM_KIND C MM_INDEX 2 3 7 9 12 14 16 20 24 32 &END QM_KIND &QM_KIND H MM_INDEX 6 10 13 15 17 19 21 23 25 26 252 253 306 307 957 958 984 985 1041 1042 1044 1045 1518 1519 1581 1582 1845 1846 2013 2014 2073 2074 2304 2305 2538 2539 3246 3247 3480 3481 4089 4090 4125 4126 4131 4132 4974 4975 5262 5263 5442 5443 5481 5482 5655 5656 &END QM_KIND &QM_KIND N MM_INDEX 1 5 &END QM_KIND &QM_KIND O MM_INDEX 4 8 11 18 22 27 29 30 31 33 34 251 305 956 983 1040 1043 1517 1580 1844 2012 2072 2303 2537 3245 3479 4088 4124 4130 4973 5261 5441 5480 5654 &END QM_KIND &QM_KIND P MM_INDEX 28 &END QM_KIND &END QMMM #........................................................... &SUBSYS &CELL ABC [angstrom] 37.9474 37.8769 37.9203 PERIODIC XYZ &END CELL &KIND H BASIS_SET aug-TZV2P-GTH POTENTIAL GTH-BLYP-q1 &END KIND &KIND O BASIS_SET aug-TZV2P-GTH POTENTIAL GTH-BLYP-q6 &END KIND &KIND N BASIS_SET aug-TZV2P-GTH POTENTIAL GTH-BLYP-q5 &END KIND &KIND C BASIS_SET aug-TZV2P-GTH POTENTIAL GTH-BLYP-q4 &END KIND &KIND P BASIS_SET aug-TZV2P-GTH POTENTIAL GTH-BLYP-q5 &END KIND &TOPOLOGY COORDINATE PDB COORD_FILE_NAME ./omp_lig_af_400step.pdb CONNECTIVITY UPSF CONN_FILE_NAME ./omp_lig_c_autopsf_solv_ions.psf &END &END SUBSYS &END FORCE_EVAL #**************************************************************** &GLOBAL PROJECT omp_lig_md RUN_TYPE MD PRINT_LEVEL MEDIUM &END GLOBAL #************************************************************** &MOTION &MD ENSEMBLE NVT STEPS 40000 TIMESTEP 0.5 TEMPERATURE 300 &THERMOSTAT &NOSE LENGTH 4 YOSHIDA 9 TIMECON 1000 MTS 2 &END NOSE &END THERMOSTAT &PRINT &ENERGY &EACH MD 1 &END EACH &END ENERGY &END PRINT &END MD &PRINT &RESTART &EACH MD 100 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &TRAJECTORY SILENT FORMAT DCD &EACH MD 1 &END EACH &END TRAJECTORY &VELOCITIES OFF LOG_PRINT_KEY T FORMAT XYZ UNIT angstrom &EACH MD 10 &END EACH ADD_LAST NUMERIC &END VELOCITIES &FORCES OFF &END FORCES &END PRINT &END MOTION #....................END...................................... </div>My QM system comprises of an organic molecule and 23 quantum water molecules in a QM box of 20x20x20. </div>While running the simulation, it showing very high temperature and then getting terminated with error <div><div>****************************************************************** *** ERROR in build_neighbor_lists (MODULE fist_neighbor_lists) *** ****************************************************************** *** GEOMETRY wrong or EMAX_SPLINE too small! *** *** Program stopped at line number 623 of MODULE fist_neighbor_lists *** ===== Routine Calling Stack ===== 7 build_neighbor_lists 6 build_fist_neighbor_lists 5 list_control 4 fist_force_control 3 velocity_verlet 2 qs_mol_dyn_low 1 CP2K CP2K| Abnormal program termination, stopped by process number 2 rank 2 in job 1 cauvery_33033 caused collective abort of all ranks exit status of rank 2: return code 1 </div><div>I don't know why it is telling the geometry is wrong. </div><div>Tarak </div><div>Molecular Simulations Lab. </div><div>JNCASR </div><div>Bangalore, India </div><div> </div></div></div> </blockquote></div> </div></div>