[CP2K:384] Block after " Adding QM/MM electrostatic....."
Teodoro Laino
teodor... at gmail.com
Sun Nov 4 09:49:42 UTC 2007
Ciao Luca,
it could be everything and " Adding QM/MM electrostatic....." is only
the latest thing buffered out from cp2k.
It could be a bug. So please you should send me:
1) PSF file
2) POT file
3) PDB file
4) Input file
5) BASIS_SET and POTENTIAL files
Please put all the files in a .tgz archive.
I will wait these files to look further into the problem.
Teo
On 4 Nov 2007, at 10:44, Luca wrote:
>
> Hi all,
> when i run my MD i have strange behavior after 94 steps of MD.
> It seems infinite loop in
> " Adding QM/MM electrostatic potential to the Kohn-Sham potential.."
> in SCF procedure (see output).
> I tried some check but nothing to do.
> I noted the similar behavior on GEOP_OPT with CG procedure(not
> reported).
> The minimization with LBFGS is ok.
> Follows input section and latest step
> Thanks in advance.
> Luca
>
> &FORCE_EVAL
> METHOD QMMM
> &DFT
> BASIS_SET_FILE_NAME GTH_BASIS_SETS
> POTENTIAL_FILE_NAME GTH_POTENTIALS
>
> &MGRID
> COMMENSURATE
> CUTOFF 300
>
> &QS
> MAP_CONSISTENT
> EXTRAPOLATION PS
> EPS_DEFAULT 1.0E-10
> EXTRAPOLATION_ORDER 3
> &END QS
>
> &SCF
> MAX_SCF 150
> EPS_SCF 1.0E-6
> SCF_GUESS ATOMIC
> &END SCF
>
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &END XC
>
> &END DFT
>
> &MM
> &FORCEFIELD
> PARM_FILE_NAME ./par_amber2charmm.inp
> PARMTYPE CHM
> EI_SCALE14 0.8333
> VDW_SCALE14 1.0
> &SPLINE
> UNIQUE_SPLINE T
> RCUT_NB 10.0
> &END SPLINE
> &END FORCEFIELD
>
> &POISSON
> &EWALD
> EWALD_TYPE NONE
> ALPHA 0.44
> GMAX 64
> O_SPLINE 6
> &END EWALD
> PERIODIC NONE
> &END POISSON
>
> &END MM
>
> &QMMM
> MM_POTENTIAL_FILE_NAME MM_POTENTIAL
> &CELL
> UNITS ANGSTROM
> ABC 12.0 12.0 18.0
> PERIODIC NONE
> &END CELL
> NOCOMPATIBILITY T
> E_COUPL GAUSS
> USE_GEEP_LIB 10
>
> &MM_KIND H
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HO
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HS
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HC
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND H1
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND H2
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND H3
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HP
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HA
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND H4
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND H5
> RADIUS 0.44
> &END MM_KIND
> &MM_KIND HW
> RADIUS 0.44
> &END MM_KIND
>
> &MM_KIND O
> RADIUS 0.73
> &END MM_KIND
> &MM_KIND O2
> RADIUS 0.73
> &END MM_KIND
> &MM_KIND OW
> RADIUS 0.73
> &END MM_KIND
> &MM_KIND OH
> RADIUS 0.73
> &END MM_KIND
> &MM_KIND OS
> RADIUS 0.73
> &END MM_KIND
>
> &MM_KIND CT
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CA
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND C
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CM
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CS
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CB
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CC
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CN
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CK
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CQ
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CW
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CV
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CR
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CX
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CY
> RADIUS 0.77
> &END MM_KIND
> &MM_KIND CD
> RADIUS 0.77
> &END MM_KIND
>
> &MM_KIND N
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND NA
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND NB
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND NC
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND N2
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND N3
> RADIUS 0.75
> &END MM_KIND
> &MM_KIND NS
> RADIUS 0.75
> &END MM_KIND
>
> &MM_KIND S
> RADIUS 1.02
> &END MM_KIND
> &MM_KIND SH
> RADIUS 1.02
> &END MM_KIND
>
> &QM_KIND C
> MM_INDEX 4631 4632 4635
> MM_INDEX 4636 4637 4638
> MM_INDEX 4639 4640 4641 4642 4643 4644
> MM_INDEX 1297
> MM_INDEX 4099 4104 4106
> &END QM_KIND
>
> &QM_KIND H
> MM_INDEX 4645 4646 4647 4648 4649 4650
> MM_INDEX 4651 4652 4653 4654 4655
> MM_INDEX 4656 4657 4658 4659 4660
> MM_INDEX 1301 1298 1299
> MM_INDEX 4105 4098 4107
> &END QM_KIND
>
> &QM_KIND O
> MM_INDEX 4633 4634
> MM_INDEX 1300
> &END QM_KIND
>
> &QM_KIND N
> MM_INDEX 4097 4103
> &END QM_KIND
>
> &LINK
> ALPHA 1.20
> LINK_TYPE IMOMM
> MM_INDEX 1295
> QM_INDEX 1297
> &END LINK
>
> &LINK
> ALPHA 1.20
> LINK_TYPE IMOMM
> MM_INDEX 4100
> QM_INDEX 4099
> &END LINK
> &END QMMM
>
> &SUBSYS
>
> &CELL
> ABC 64.000 64.0 57.000
> UNIT ANGSTROM
> PERIODIC NONE
> &END CELL
>
> &TOPOLOGY
> COORD_FILE_NAME As_THI_T2.pdb
> COORDINATE PDB
> CONN_FILE_NAME As.psf
> CONNECTIVITY PSF
> &END TOPOLOGY
>
> &KIND H
> BASIS_SET TZV2P-GTH # DZVP-GTH #
> POTENTIAL GTH-BLYP-q1
> &END KIND
>
> &KIND
> O
> BASIS_SET TZV2P-GTH # DZVP-GTH #
> POTENTIAL GTH-BLYP-q6
> &END
> KIND
>
> &KIND
> C
> BASIS_SET TZV2P-GTH # DZVP-GTH #
> POTENTIAL GTH-BLYP-q4
> &END
> KIND
>
> &KIND
> N
> BASIS_SET TZV2P-GTH # DZVP-GTH #
> POTENTIAL GTH-BLYP-q5
> &END
> KIND
>
> &KIND
> S
> BASIS_SET TZV2P-GTH # DZVP-GTH #
> POTENTIAL GTH-BLYP-q6
> &END KIND
>
> &COLVAR
> &DISTANCE
> ATOMS 4632 1300
> &END DISTANCE
> &END COLVAR
>
> &COLVAR
> &DISTANCE
> ATOMS 4634 4103
> &END DISTANCE
> &END COLVAR
>
> &COLVAR
> &DISTANCE
> ATOMS 1300 1301
> &END DISTANCE
> &END COLVAR
>
> &COLVAR
> &DISTANCE
> ATOMS 1300 4103
> &END DISTANCE
> &END COLVAR
>
> &END SUBSYS
> &END FORCE_EVAL
>
> &GLOBAL
> PRINT_LEVEL MEDIUM
> PROJECT AS_THI_T2
> RUN_TYPE MD
> SAVE_MEM F
> &END GLOBAL
>
> &MOTION
>
> &GEO_OPT
> OPTIMIZER CG
> MAX_ITER 125
> RMS_DR 1.0E-02
> MAX_DR 1.0E-02
> RMS_FORCE 1.0E-02
> MAX_FORCE 1.0E-02
> &END GEO_OPT
>
> &MD
> ENSEMBLE NVE
> STEPS 1000
> TIMESTEP 0.20
> TEMPERATURE 20.0
> TEMP_TOL 1.0
> ANNEALING 1.0
> &END MD
>
> &PRINT
> &RESTART OFF
> &END
> &RESTART_HISTORY OFF
> &END
>
> &TRAJECTORY
> EACH 1
> FORMAT XMOL
> &END
>
> &VELOCITIES OFF
> &END
> &END PRINT
>
> &CONSTRAINT
>
> # &COLLECTIVE
> # COLVAR 1
> # INTERMOLECULAR T
> # TARGET [angstrom] 1.46
> # &END COLLECTIVE
>
> # &COLLECTIVE
> # COLVAR 2
> # INTERMOLECULAR T
> # TARGET [angstrom] 3.22
> # &END COLLECTIVE
>
> # &COLLECTIVE
> # COLVAR 3
> # INTERMOLECULAR T
> # TARGET [angstrom] 2.34
> # &END COLLECTIVE
>
> # &COLLECTIVE
> # COLVAR 4
> # INTERMOLECULAR T
> # TARGET [angstrom] 3.16
> # &END COLLECTIVE
>
>
> &FIXED_ATOMS
> # Residues within 5 ang. to QM region are free to move,
> # other residues are
> # fixed
> LIST 1
> LIST 2
> LIST 3
> LIST 4
> ......
> ......
>
>
> **********************************************************************
> *********
> ENSEMBLE TYPE
> = nve
> STEP NUMBER
> = 94
> TIME [FS] =
> 18.800000
> CONSERVED QNTY =
> -0.184128334053E+03
>
> INSTANTANEOUS AVERAGES
> CPU [S] =
> 138.16 87.80
> {E-E0}/{k_b*N_at} = 0.176474183833E+01
> 0.139196951545E+01
> POTENTIAL ENERGY[hartree] = -0.184159882198E+03
> -0.184167340405E+03
> MM KINETIC ENERGY[hartree] = 0.315481442922E-01
> 0.328358730418E-01
> QM KINETIC ENERGY[hartree] = 0.397864210092E-02
> 0.434631302514E-02
> MM TEMPERATURE[K] =
> 19.139 19.921
> QM TEMPERATURE[K] =
> 18.613 20.333
>
> **********************************************************************
> *********
>
>
> Translating the system in order to center the QM fragment in the QM
> box.
> QMMM| Information on the QM/MM Electrostatic Potential:
> QMMM| QM/MM Coupling computed collocating the Gaussian Potential
> Functions.
> MM DIPOLE BERRY PHASE ( A.U.)| 6.055006
> 4.833916 8.639664
> MM DIPOLE BERRY PHASE (Debye)| 15.390288 12.286586
> 21.959832
> MM DIPOLE (NON BERRY PHASE) DERIVATIVE (A.U.)| -0.000156
> 0.000728 0.000320
>
>
> DISTRIBUTION OF THE NEIGHBOR LISTS
>
> Process Number of particle pairs Number of matrix elements
>
> 0 112 28351
> 1 107 28856
> 2 149 29242
> 3 143 28990
> 4 105 29968
> 5 100 29953
> 6 146 27725
> 7 140 29319
>
> Sum 1002 232404
>
>
> DISTRIBUTION OF THE OVERLAP MATRIX
>
> Process Number of matrix blocks Number of matrix elements
>
> 0 112 28351
> 1 107 28856
> 2 149 29242
> 3 143 28990
> 4 105 29968
> 5 100 29953
> 6 146 27725
> 7 140 29319
>
> Sum 1002 232404
>
> of 1035 ( 96.8 % occupation)
>
> Number of electrons: 116
> Number of occupied orbitals: 58
> Number of orbital functions: 678
>
> Number of independent orbital functions: 678
>
> Extrapolation method: PS Nth order
>
>
> SCF WAVEFUNCTION OPTIMIZATION
>
> Step Update method Time Convergence
> Total energy
>
> ----------------------------------------------------------------------
> -------
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 1 Mixing/Diag. 0.40E+00 3.30 0.0011843927
> -148.2380772731
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 2 Mixing/Diag. 0.40E+00 4.32 0.0007784460
> -148.2380772937
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 3 DIIS/Diag. 0.89E-05 4.28 0.0004309770
> -148.2380773033
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 4 DIIS/Diag. 0.24E-04 4.31 0.0003538427
> -148.2380773182
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 5 DIIS/Diag. 0.48E-05 4.31 0.0001920630
> -148.2380773201
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 6 DIIS/Diag. 0.73E-05 4.30 0.0000690038
> -148.2380773203
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 7 DIIS/Diag. 0.28E-05 4.31 0.0000307216
> -148.2380773202
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 8 DIIS/Diag. 0.24E-05 4.30 0.0000463294
> -148.2380773204
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 9 DIIS/Diag. 0.40E-05 4.29 0.0000398251
> -148.2380773200
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 10 DIIS/Diag. 0.40E-05 4.36 0.0000346356
> -148.2380773204
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 11 DIIS/Diag. 0.15E-05 4.33 0.0000183436
> -148.2380773204
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 12 DIIS/Diag. 0.37E-06 4.31 0.0000119746
> -148.2380773205
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 13 DIIS/Diag. 0.21E-06 4.33 0.0000075848
> -148.2380773205
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
> 14 DIIS/Diag. 0.71E-06 4.30 0.0000112294
> -148.2380773205
>
> Total electronic density (r-space): -116.0000001201
> -0.0000001201
> Total core charge density (r-space): 115.9999999999
> -0.0000000001
> Total charge density (r-space):
> -0.0000001202
> Total charge density (g-space):
> -0.0000001202
> Adding QM/MM electrostatic potential to the Kohn-Sham potential..
>
>
> >
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