<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Shihao,<div> </div><div>It seems that you didn't set up explicitly any parameters for your QM simulation box... but it is impossible to say if it could be the origin of your "strange" problem because, as Teo has already pointed out, it is difficult to say something concerning your input without having some more information about the contents of your "include" files.</div><div> </div><div>Regards,</div><div> </div><div>Pablo.</div><div><div>_____________________________________________</div><div>Pablo Campomanes</div><div>Laboratory of Computational Chemistry and Biochemistry </div><div>BCH 4118 EPF Lausanne</div><div> </div><div> </div><div><div>On Feb 17, 2010, at 7:22 PM, shihao wrote:</div> <blockquote type="cite"><div>Hi there, I've been running some QM/MM simulations with periodic MM and isolated QM box (the QM box is in the center of the cell). However, some molecules tend to orient in a strange way (eg. parallel to XY, XZ or YZ plane). I'm pretty sure that this is not because of interactions from MM region. I've done all kinds of tests (different QM box sizes, wall widths, etc.) but still couldn't figure out where the problem is. Has anyone got experiences with this problem? Any clues will be greatly appreciated. Also, is it necessary to specify PERIODIC section in QMMM? I've tried it but didn't succeed. Regards, Shihao P.S. Here's the input file. I didn't provide the additional files (potential, pdb, psf, etc.), but please let me know if they are needed and I will simplify them and upload them as well. &GLOBAL PROGRAM_NAME CP2K PROJECT_NAME project RUN_TYPE MD SEED 1000 PREFERRED_FFT_LIBRARY FFTW PRINT_LEVEL LOW SAVE_MEM &END GLOBAL &FORCE_EVAL METHOD QMMM &DFT BASIS_SET_FILE_NAME ./GTH_BASIS_SETS POTENTIAL_FILE_NAME ./POTENTIAL CHARGE 1 MULTIPLICITY 1 UNRESTRICTED_KOHN_SHAM F &SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-6 MAX_SCF 50 &OUTER_SCF MAX_SCF 10 &END OUTER_SCF &OT PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS N_DIIS 7 &END OT &PRINT &RESTART &EACH MD 20 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &END PRINT &END SCF &QS METHOD GPW EPS_DEFAULT 1.0E-12 EXTRAPOLATION ASPC &END QS &MGRID COMMENSURATE CUTOFF 280 &END MGRID &POISSON POISSON_SOLVER MT PERIODIC NONE &END POISSON &XC &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &XC_GRID XC_SMOOTH_RHO NN10 XC_DERIV SPLINE2_SMOOTH &END XC_GRID &END XC &PRINT &E_DENSITY_CUBE &EACH MD 20 &END EACH &END E_DENSITY_CUBE &END PRINT &END DFT &MM &FORCEFIELD PARMTYPE CHM PARM_FILE_NAME ./par_all27_prot_lipid_amm.prm &SPLINE RCUT_NB 12.0 &END SPLINE &END FORCEFIELD &POISSON &EWALD EWALD_TYPE SPME ALPHA 0.35 GMAX 80 80 80 O_SPLINE 6 &END EWALD &END POISSON &END MM &QMMM USE_GEEP_LIB 7 E_COUPL GAUSS @INCLUDE run_001_cp2k.inp @INCLUDE mm_kinds &WALLS TYPE REFLECTIVE WALL_SKIN 0.5 &END WALLS &PERIODIC GMAX 0.1 &MULTIPOLE RCUT 30.0 EWALD_PRECISION 0.000001 &END &END &PRINT &PROGRAM_RUN_INFO SILENT &END PROGRAM_RUN_INFO &PERIODIC_INFO SILENT &END PERIODIC_INFO &QMMM_LINK_INFO SILENT &END QMMM_LINK_INFO &END PRINT &END QMMM &SUBSYS &CELL ABC 92.3237 77.4554 91.24 PERIODIC XYZ &END CELL &TOPOLOGY CONNECTIVITY UPSF CONN_FILE_NAME ./build.xplor_psf COORDINATE PDB COORD_FILE_NAME ./run_001_cp2k.pdb PARA_RES T &END TOPOLOGY ######################################## Basis sets and pseudopotentials &KIND H BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q1 &END KIND &KIND C BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q4 &END KIND &KIND N BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q5 &END KIND &KIND O BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q6 &END KIND &END SUBSYS &END FORCE_EVAL &MOTION &MD ENSEMBLE LANGEVIN STEPS 2000 TIMESTEP 0.50 TEMPERATURE 298.15 &LANGEVIN GAMMA 0.004 &END &PRINT &ENERGY &EACH MD 20 &END EACH &END ENERGY &END PRINT &END MD &PRINT &RESTART &EACH MD 20 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &TRAJECTORY SILENT FORMAT DCD &EACH MD 20 &END EACH &END TRAJECTORY &VELOCITIES OFF &END VELOCITIES &FORCES OFF &END FORCES &END PRINT &CONSTRAINT &HBONDS EXCLUDE_QM T &END HBONDS SHAKE_TOLERANCE 1.0E-9 &LAGRANGE_MULTIPLIERS ON COMMON_ITERATION_LEVELS 3 &END LAGRANGE_MULTIPLIERS &END CONSTRAINT &END MOTION -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en">http://groups.google.com/group/cp2k?hl=en</a>. </div></blockquote></div> </div></body></html>