NAMD equil CP2K QM/MM
tarak karmakar
tarak... at gmail.com
Sat Mar 15 06:23:33 UTC 2014
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.
Any suggestion?
On Fri, Mar 14, 2014 at 11:08 AM, tarak karmakar <tarak... at gmail.com>wrote:
> Dear All,
>
> 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.
>
> 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......................................
>
>
> My QM system comprises of an organic molecule and 23 quantum water
> molecules in a QM box of 20x20x20.
>
> While running the simulation, it showing very high temperature and then
> getting terminated with error
>
>
>
> ******************************************************************
> *** 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
>
> I don't know why it is telling the geometry is wrong.
>
>
>
> Tarak
> Molecular Simulations Lab.
> JNCASR
> Bangalore, India
>
>
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