Wavelet and MT errors due to box size
Dries Van Rompaey
dries.va... at gmail.com
Tue Sep 19 20:24:55 UTC 2017
Hi everyone,
I'm seeing extreme increases in energy during SCF in my QMMM system. It's a
protein:ligand complex which I have previously simulated using
semi-empirical QMMM (with PM6), but I am having difficulties moving it to
DFT. Problems occur both using wavelet and MT as poisson-solver.
Using wavelet, the SCF optimisation prints out:
> 1 OT CG 0.15E+00 6.3 0.13953650 -490.9063955586 -4.91E+02
> *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the ***
> *** edges of the unit cell: wrong results in WAVELET solver ***
> 2 OT LS 0.30E+00 3.3 ********************
> *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the ***
> *** edges of the unit cell: wrong results in WAVELET solver ***
> 3 OT CG 0.30E+00 10.0 1.1529+103 ******************** 1.51+106
Using MT:
> 1 OT CG 0.15E+00 4.3 0.07338929 -245.3521031334 -2.45E+02
> 2 OT LS 0.16E-01 2.1 -105.1518004766
> 3 OT CG 0.16E-01 3.9 0.08689260 -214.7379955081 3.06E+01
> 4 OT LS 0.16E-03 2.0 589356.6222967544
> 5 OT CG 0.16E-03 3.8 1.58848424 34863.9952881550 3.51E+04
> 6 OT LS 0.16E-05 2.0 474895064.4618470073
> 7 OT CG 0.16E-05 3.9 87.13775893 45190083.4925281629 4.52E+07
> 8 OT LS 0.16E-07 2.0 ********************
> 9 OT CG 0.16E-07 3.8 9824.70615457 ******************** 4.98E+10
I have tried to increase the size of the QM box, but my box is now at
45x45x45 Å and my molecule is no longer than 17 Å. As far as I can tell
from the posts on the mailing list, this box size should be sufficient to
contain the system. All files can be found on the dropbox link here:
https://www.dropbox.com/sh/33lm80977zedcua/AADsNbFIpm_hmyvS1N_xF5DBa?dl=0
My input file is:
&GLOBAL
PROJECT METADYN_DFT
PRINT_LEVEL LOW
RUN_TYPE MD
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME GTH_POTENTIALS
CHARGE 1
MULTIPLICITY 1
&SCF
MAX_SCF 30
EPS_SCF 1.0E-6
SCF_GUESS ATOMIC
&OT
MINIMIZER CG
PRECONDITIONER FULL_ALL
&END OT
&OUTER_SCF
MAX_SCF 20
EPS_SCF 1.0E-6
&END OUTER_SCF
&END SCF
&MGRID
CUTOFF 320
COMMENSURATE
NGRIDS 4
&END MGRID
&QS
&END QS
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&POISSON
PERIODIC NONE
POISSON_SOLVER WAVELET
&END POISSON
&END DFT
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME complex_ljmod.prmtop
&SPLINE
EMAX_SPLINE 1.0E8
RCUT_NB [angstrom] 10
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 80
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC [angstrom] 79.0893744057 79.0893744057 79.0893744057
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&TOPOLOGY
&CENTER_COORDINATES
&END
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME complex_ljmod.prmtop
&END TOPOLOGY
&KIND P
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND N
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND H
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND Cl-
ELEMENT Cl
&END KIND
&KIND NU
ELEMENT N
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&KIND NS
ELEMENT N
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&END SUBSYS
&QMMM
ECOUPL GAUSS
USE_GEEP_LIB 10
&CELL
ABC [angstrom] 45 45 45
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&QM_KIND O
MM_INDEX 3236
MM_INDEX 3237
MM_INDEX 3238
MM_INDEX 3242
MM_INDEX 3257
&END QM_KIND
&QM_KIND H
MM_INDEX 3223
MM_INDEX 3226
MM_INDEX 3227
MM_INDEX 3228
MM_INDEX 3229
MM_INDEX 3232
MM_INDEX 3233
MM_INDEX 3240
MM_INDEX 3244
MM_INDEX 3245
MM_INDEX 3246
MM_INDEX 3247
MM_INDEX 3249
MM_INDEX 3251
MM_INDEX 3254
MM_INDEX 3256
MM_INDEX 3259
MM_INDEX 3261
MM_INDEX 3263
MM_INDEX 3266
MM_INDEX 3268
MM_INDEX 3270
MM_INDEX 3272
MM_INDEX 3274
MM_INDEX 3277
MM_INDEX 3279
&END QM_KIND
&QM_KIND P
MM_INDEX 3235
&END QM_KIND
&QM_KIND C
MM_INDEX 3221
MM_INDEX 3230
MM_INDEX 3231
MM_INDEX 3234
MM_INDEX 3241
MM_INDEX 3243
MM_INDEX 3248
MM_INDEX 3250
MM_INDEX 3252
MM_INDEX 3253
MM_INDEX 3255
MM_INDEX 3258
MM_INDEX 3260
MM_INDEX 3262
MM_INDEX 3264
MM_INDEX 3265
MM_INDEX 3267
MM_INDEX 3269
MM_INDEX 3271
MM_INDEX 3273
MM_INDEX 3275
MM_INDEX 3276
MM_INDEX 3278
&END QM_KIND
&QM_KIND N
MM_INDEX 3222
MM_INDEX 3224
MM_INDEX 3225
MM_INDEX 3239
&END QM_KIND
&END QMMM
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
TIMESTEP [fs] 0.5
STEPS 100
TEMPERATURE 298
&THERMOSTAT
TYPE NOSE
REGION GLOBAL
&NOSE
TIMECON [fs] 100.
&END NOSE
&END THERMOSTAT
&END MD
&PRINT
&RESTART ! This section controls the
printing of restart files
&EACH ! A restart file will be
printed every 10000 md steps
MD 5000
&END
&END
&RESTART_HISTORY ! This section controls
dumping of unique restart files during the run keeping all of them.Most
useful if recovery is needed at a later point.
&EACH ! A new restart file will
be printed every 10000 md steps
MD 5000
&END
&END
&TRAJECTORY ! Thes section Controls the
output of the trajectory
FORMAT XYZ ! Format of the output
trajectory is XYZ
&EACH ! New trajectory frame will
be printed each 100 md steps
MD 1000
&END
&END
&END PRINT
&END MOTION
&EXT_RESTART
RESTART_FILE_NAME NPT-1.restart
RESTART_COUNTERS .FALSE.
&END
Thanks for your time,
Kind regards,
Dries
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