<div dir="ltr">Any suggestions? <div class="gmail_extra"> <div class="gmail_quote">On Fri, Feb 21, 2014 at 2:00 PM, 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>Dear All, </div>I have set up a QM/MM system by taking an organic molecule in 40x40x40 water box. The quantum region contains the organic molecule and 23 water molecules in a periodic box of 25x25x25 ang^3. Then I am trying to run a short NVT, the input 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 EPS_SCF 1.0e-7 MAX_SCF 250 ## initial wavefunction guess. If no restart file, does atomic? SCF_GUESS RESTART ##atomic,restart,random,or core ## Orbital transformation method helps converge more rapidly &OT ON ## precondition the matrix with the kinetic energy. Helps diagonalize quick PRECOND_SOLVER INVERSE_CHOLESKY PRECONDITIONER FULL_KINETIC ## Use a conjugate gradient minimizer 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 37 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 &CELL ABC [angstrom] 20.0 20.0 20.0 PERIODIC XYZ &END CELL &PERIODIC GMAX 1 &MULTIPOLE EWALD_PRECISION 0.000001 RCUT 30.0 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 26 171 172 756 757 960 961 1440 1441 1929 1930 2028 2029 2097 2098 2385 2386 2403 2404 2631 2632 2802 2803 2865 2866 2877 2878 3408 3409 3528 3529 3537 3538 3633 3634 3684 3685 3783 3784 4431 4432 4719 4720 4860 4861 5331 5332 &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 34 170 755 959 1439 1928 2027 2096 2384 2402 2630 2801 2864 2876 3407 3527 3536 3632 3683 3782 4430 4718 4859 5330 &END QM_KIND &QM_KIND P MM_INDEX 28 &END QM_KIND &END QMMM #........................................................... &SUBSYS &CELL ABC [angstrom] 39.327 39.254 39.299 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_200ps_NPT.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 3 YOSHIDA 3 TIMECON 2000 MTS 2 &END NOSE &END &PRINT &ENERGY &EACH MD 100 &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 100 &END EACH &END TRAJECTORY &VELOCITIES OFF LOG_PRINT_KEY T FORMAT XYZ UNIT angstrom &EACH MD 100 &END EACH ADD_LAST NUMERIC &END VELOCITIES &FORCES OFF &END FORCES &END PRINT &END MOTION #....................END...................................... At the first NVT step the temperature of the system is very high ******************************************************************************* ENSEMBLE TYPE = NVT STEP NUMBER = 1 TIME [fs] = 0.500000 CONSERVED QUANTITY [hartree] = -0.589910746226E+03 INSTANTANEOUS AVERAGES CPU TIME [s] = 5909.45 5909.45 ENERGY DRIFT PER ATOM [K] = 0.499380591190E+04 0.000000000000E+00 POTENTIAL ENERGY[hartree] = -0.687025973983E+03 -0.687025973983E+03 TOTAL KINETIC ENERGY[hartree]= 0.971145351369E+02 0.971145351369E+02 QM KINETIC ENERGY[hartree] = 0.891156598761E+02 0.891156598761E+02 TOTAL TEMPERATURE[K] = 3579.168 3579.168 QM TEMPERATURE[K] = 182138.939 182138.939 ******************************************************************************* and then after few steps the job is coming out with the following error *** ERROR in build_neighbor_lists *** * *** GEOMETRY wrong or EMAX_SPLINE too small! *** </div><div>Note: Based on previous mailing list, increase in the EMAX_SPLINE value did not help me. Any suggestions will be appreciated. regards, Tarak</div>Molecular Simulation Lab. JNCASR, Bangalore, India</div> </blockquote></div> </div></div>