Block after " Adding QM/MM electrostatic....."
Luca
bellu... at unisi.it
Sun Nov 4 10:02:39 UTC 2007
Ciao Teo,
thanks for fast response..
Ok. I work for you request..
at this moment I tried to run with HIGH printing and
program block at first step after SCF
.....
.........
19 DIIS/Diag. 0.95E-06 4.39 0.0000008858
-148.2044296893
*** SCF run converged in 19 steps ***
Total electronic density (r-space): -116.0000002903
-0.0000002903
Total core charge density (r-space): 116.0000000000
0.0000000000
Total charge density (r-space):
-0.0000002903
Total charge density (g-space):
-0.0000002903
Overlap energy of the core charge distribution:
0.00000839724822
Self energy of the core charge distribution:
-422.48901359943301
Core Hamiltonian energy:
129.97430504509265
Hartree energy:
171.41209987875129
Exchange-correlation energy:
-51.57087955822965
Coulomb Electron-Electron Interaction Energy
- Already included in the total Hartree term
409.92475143294126
QM/MM Electrostatic energy:
24.4690501472
Total energy:
-148.20442968933276
Mulliken charges : iteration level:
1_0
...........................................
127 5888.55511261962 0.1009E-02 0.2658E-04
128 5888.55511257744 0.9661E-03 0.2544E-04
Wannier localization finished in 128 iterations
D Eq. 11 1 14.3042429464
D Eq. 11 2 13.5761904129
D Eq. 11 3 9.5879832646
CP2K| Stopped by processor
number 0
CP2K| mpi_allreduce @ mp_min_rv
CP2K| Error number was
134808585
Tahnks
On Nov 4, 10:49 am, Teodoro Laino <teodor... at gmail.com> wrote:
> 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
>
> ...
>
> read more »
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