<div dir="ltr">Hi,<div><br></div><div>Just to add Samuel's reply.</div><div><br></div><div>To reduce the volume of the output file, you need to set the keyword PRINT_LEVEL to LOW in the &GLOBAL section.</div><div><br></div><div><font color="#0000ff">&GLOBAL</font></div><div><font color="#0000ff"> ...</font></div><div><font color="#0000ff"> PRINT_LEVEL LOW<br> ...</font></div><div><font color="#0000ff">&END GLOBAL</font></div><div><br></div><div>As mentioned by Samuel, you can extract the trajectory into the *.xyz file by setting the &PRINT keyword in the &MOTION section. The name of the trajectory file is the same as the PROJECT name in the &GLOBAL section you given, but with the extension of *-pos-1.xyz.</div><div><br></div><div><font color="#0000ff">&MOTION</font></div><div><font color="#0000ff"> ...</font></div><div><font color="#0000ff"> &PRINT</font></div><div><font color="#0000ff"> ...</font></div><div><font color="#0000ff"> &TRAJECTORY</font></div><div><font color="#0000ff"> LOG_PRINT_KEY TRUE</font></div><div><font color="#0000ff"> FORMAT XYZ</font></div><div><font color="#0000ff"> UNIT angstrom</font></div><div><font color="#0000ff"> &EACH</font></div><div><font color="#0000ff"> MD 1 </font><font color="#000000"># It depends on your system. Maybe you can set it as 10, which means to save the coordinates every 10 steps.</font></div><div><font color="#0000ff"> &END EACH</font></div><div><font color="#0000ff"> ADD_LAST NUMERIC</font></div><div><font color="#0000ff"> &END TRAJECTORY</font></div><div><font color="#0000ff"> ...</font></div><div><font color="#0000ff"> &END PRINT</font></div><div><font color="#0000ff">&END MOTION</font></div><div><br></div><div>I never run QM/MM, so I could not give any suggestion on your second question.</div><div><br></div><div>Regards,</div><div>Huan</div><div>.</div><div><br></div><div><br>On Saturday, July 30, 2016 at 6:58:50 PM UTC+3, tuf...@temple.edu wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hello CP2K users,<br>I am running QMMM simulation of 1 di alanine in 5000 methanol molecules. My system deals with alanine and 25 methanol molecule in QM region and rest in MM region using the attached input file. <br>I want to know why my alanine.out file is huge as for only 1000 steps it is ~3 GB.<br>My main question is that is this input file is good enough to start qmmm or i need some additional parameters....<br>I hv doubt about some key point mentioned in input file in<span style="color:rgb(255,0,0)"><b> bold red<br>Thank you <br></b></span><br>&FORCE_EVAL<br> METHOD QMMM<br>#-----------------------------<wbr>------------------------------<wbr>-------------------<br> &DFT<br> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS<br> POTENTIAL_FILE_NAME ./GTH_POTENTIALS<br> &MGRID<br> COMMENSURATE<br> CUTOFF 300<br> &END MGRID<br> &QS<br> &END QS<br> &SCF<br> # SCF_GUESS atomic<br> MAX_SCF 30<br> EPS_SCF 1.0E-6<br> SCF_GUESS ATOMIC<br> &OUTER_SCF<br> EPS_SCF 1.0E-6<br> MAX_SCF 10<br> &END OUTER_SCF<br> &OT<br> PRECONDITIONER FULL_SINGLE_INVERSE<br> MINIMIZER DIIS<br> &END OT<br> &PRINT<br> &RESTART<br> &EACH<br> MD 10<br> &END EACH<br> FILENAME =ABC.RESTART<br> &END RESTART<br> &RESTART_HISTORY OFF<br> &END RESTART_HISTORY<br> &END PRINT<br> &END SCF<br> &XC<br> &XC_GRID<br> XC_SMOOTH_RHO NN10<br> XC_DERIV NN10_SMOOTH<br> &END XC_GRID<br> &XC_FUNCTIONAL BLYP<br> &END XC_FUNCTIONAL<br> &vdW_POTENTIAL<br> POTENTIAL_TYPE PAIR_POTENTIAL<br> &PAIR_POTENTIAL<br> TYPE DFTD3<br> PARAMETER_FILE_NAME ./dftd3.dat<br> REFERENCE_FUNCTIONAL BLYP<br> CALCULATE_C9_TERM .TRUE.<br> REFERENCE_C9_TERM .TRUE.<br> &END PAIR_POTENTIAL<br> &END vdW_POTENTIAL<br> &END XC<br> &END DFT<br>#-----------------------------<wbr>------------------------------<wbr>-------------------<br> &MM<br> &FORCEFIELD<br> PARM_FILE_NAME ala_big.top<br> PARMTYPE AMBER<br> &SPLINE<br> EMAX_SPLINE 1.0 <span style="color:rgb(255,0,0)"><b># is it enough or need higher how to check </b></span><br> RCUT_NB 10<br> &END<br> &END FORCEFIELD<br> &POISSON<br> &EWALD<br> EWALD_TYPE ewald<br> ALPHA .44<br> GMAX 21<br> &END EWALD<br> &END POISSON<br> &END MM<br>#-----------------------------<wbr>------------------------------<wbr>-------------------<br> &QMMM<br> &CELL<br> ABC 25.0 25.0 25.0 <b><span style="color:rgb(255,0,0)"># it will be periodic or not most confusing for me .....</span></b><br> &END CELL<br><span style="color:rgb(255,0,0)"> <span style="color:rgb(0,0,0)">ECOUPL GAUSS <br> USE_GEEP_LIB 7</span> <b># why 7 i just got the range from cp2k manual 0-15</b></span><br> &QM_KIND O<br> MM_INDEX 8 18 669 3081 3609 3813 4563 6375 9261 10821 11295 12795<br> MM_INDEX 13029 13053 13551 13695 14979 15069 17613 17853 18447 18471<br> MM_INDEX 18891 19809 19875 25971 26709<br> &END QM_KIND<br> &QM_KIND N<br> MM_INDEX 5 15<br> &END QM_KIND<br> &QM_KIND C<br> MM_INDEX 1 7 9 10 17 19 666 3078 3606 3810 4560 6372 9258 10818 11292<br> MM_INDEX 12792 13026 13050 13548 13692 14976 15066 17610 17850 18444<br> MM_INDEX 18468 18888 19806 19872 25968 26706<br> &END QM_KIND<br> &QM_KIND H<br> MM_INDEX 2 3 4 6 11 12 13 14 16 20 21 22<br> &END QM_KIND<br> &QM_KIND H<br> MM_INDEX 665 3077 3605 3809 4559 6371 9257 10817 11291 12791 13025 13049<br> MM_INDEX 13547 13691 14975 15065 17609 17849 18443 18467 18887 19805 19871 25967 26705<br> &END QM_KIND<br> &QM_KIND H<br> MM_INDEX 667 3079 3607 3811 4561 6373 9259 10819 11293 12793 13027 13051 13549<br> MM_INDEX 13693 14977 15067 17611 17851 18445 18469 18889 19807 19873 25969 26707<br> &END QM_KIND<br> &QM_KIND H<br> MM_INDEX 668 3080 3608 3812 4562 6374 9260 10820 11294 12794 13028 13052 13550<br> MM_INDEX 13694 14978 15068 17612 17852 18446 18470 18890 19808 19874 25970 26708<br> &END QM_KIND<br> &QM_KIND H<br> MM_INDEX 670 3082 3610 3814 4564 6376 9262 10822 11296 12796 13030 13054 13552 13696<br> MM_INDEX 14980 15070 17614 17854 18448 18472 18892 19810 19876 25972 26710<br> &END QM_KIND<br> &END QMMM<br>#-----------------------------<wbr>------------------------------<wbr>-------------------<br> &SUBSYS<br> &CELL<br> <span style="color:rgb(255,0,0)"><span style="color:rgb(0,0,0)">ABC 67.283 67.283 67.283 </span><b># it should be periodic or not .....</b></span><br> &END CELL<br> &TOPOLOGY<br> COORDINATE CRD<br> COORD_FILE_NAME ./ala_big.crd<br> CONNECTIVITY AMBER<br> CONN_FILE_NAME ./ala_big.top<br> &END<br> &KIND H<br> BASIS_SET TZV2P-GTH<br> POTENTIAL GTH-BLYP-q1<br> MASS 2.0<br> &END KIND<br> &KIND O<br> BASIS_SET TZV2P-GTH<br> POTENTIAL GTH-BLYP-q6<br> &END KIND<br> &KIND C<br> BASIS_SET TZV2P-GTH<br> POTENTIAL GTH-BLYP-q4<br> &END KIND<br> &KIND N<br> BASIS_SET TZV2P-GTH<br> POTENTIAL GTH-BLYP-q5<br> &END KIND<br> &END SUBSYS<br>&END FORCE_EVAL<br>#-----------------------------<wbr>------------------------------<wbr>-------------------<br>&GLOBAL<br> PROJECT ALANINE<br> RUN_TYPE MD<br>&END GLOBAL<br>&MOTION<br> &MD<br> ENSEMBLE NVT<br> STEPS 1000<br> TIMESTEP 1.0<br> TEMPERATURE 300<br> &THERMOSTAT<br> TYPE CSVR<br> &CSVR<br> TIMECON 20<br> &END CSVR<br> &END THERMOSTAT<br> &PRINT<br> &ENERGY<br> &EACH<br> MD 2<br> &END EACH<br> FILENAME =ABC.ene<br> &END ENERGY<br> &END PRINT<br> &END MD<br>&END MOTION<br><br></div></blockquote></div></div>