[CP2K:5012] Periodic RESP charges for paracetamol form I crystal

Dorothea Golze dorothe... at googlemail.com
Sat Mar 1 20:19:58 UTC 2014


Hi,

the keywords "RANGE" and "LENGTH" make no sense in your case. They are for
slab-like periodic systems. The section "PERIODIC_SYS" and
"NONPERIODIC_SYS" refer to the way the fitting points are collected.
PERIODIC_SYS sets the parameter for collecting fitting points for slab-like
systems. In "NONPERIODC_SYS" fitting points are collected in spheres around
the atoms. That is what you need here. Whether a periodic RESP fit is
required or not is solely decided on the usage of a periodic or
non-periodic Poisson solver.
I admit the names of these subsection are maybe a little bit misleading. I
should change them....
There were questions about the periodic RESP charges before, see
my last post there:
https://groups.google.com/forum/#!msg/cp2k/G3THGbvvIcU/CgGZxvtbGrsJ

Kind regards,
Dorothea


2014-03-01 21:02 GMT+01:00 mbellucci <mbell... at gmail.com>:

>
> Dear CP2K Users,
>
> I am trying to calculate the RESP charges for a unit cell of the form I
> crystal of paracetamol using periodic boundary conditions using version 2.5
> of CP2K.  I have tried many different things but in every calculation, the
> RESP charges seem to be unphysical, i.e. the magnitudes of the charges seem
> to very large and most have the wrong sign.  The things I have tried in
> order to fix this include:
>
> increasing the cutoff
> changing the functional
> increasing the size of the basis set
> changing the values of the LENGTH and RANGE keywords in the PERIODIC_SYS
> section of RESP
> changing the SURF_DIRECTION in the PERIODIC_SYS section of RESP
> I've also experimented with the keywords WIDTH, RESTRAIN_HEAVIES_STRENGTH,
> and RESTRAIN_HEAVIES_TO_ZERO in RESP
>
> Nothing seems to work for the RESP charges.  However, when I turn off the
> periodic boundary conditions the calculations produce RESP charges that
> make physical sense.  Also, for calculations with or without periodic
> boundary conditions, the DDAP charges make physical sense, but I'm hesitant
> to use them in MD simulations since they are less frequently used in MD
> simulations in the literature.  If anyone could help identify an error I am
> making when calculating these RESP charges, I would greatly appreciate it!
>  Also, if anyone could comment on the reliability of DDAP charges in
> general, I would appreciate it as well.
>
> For the calculation, the coordinates of the form I crystal as well as the
> dimensions of the unit cell were obtained from the cambridge structural
> database.  The input file I'm using, the outputted RESP charges, and the
> outputted DDAP charges are the following:
>
> &GLOBAL
>   PROJECT form_1
>   RUN_TYPE ENERGY_FORCE
>   PRINT_LEVEL MEDIUM
>   WALLTIME 86400
> &END GLOBAL
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     BASIS_SET_FILE_NAME EMSL_BASIS_SETS
>     POTENTIAL_FILE_NAME POTENTIAL
>     CHARGE 0
>     MULTIPLICITY 1
>     &MGRID
>       CUTOFF 300
>       REL_CUTOFF 50
>     &END MGRID
>
>     &QS
>       METHOD GAPW
>       EPS_DEFAULT  1.0E-12
>       MAP_CONSISTENT TRUE
>       EXTRAPOLATION ASPC
>       EXTRAPOLATION_ORDER 3
>     &END QS
>
>     &SCF
>       MAX_SCF 500
>       SCF_GUESS ATOMIC
>       EPS_SCF 1.0E-7
>       &OT ON
>         MINIMIZER DIIS
>         PRECONDITIONER FULL_ALL
>         ENERGY_GAP 0.001
>       &END OT
>
>       &OUTER_SCF
>          EPS_SCF 1.0E-5
>          MAX_SCF 100
>       &END OUTER_SCF
>     &END SCF
>
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>
>
>   &SUBSYS
>     &CELL
>       ABC 12.93 9.40 7.10
>       ALPHA_BETA_GAMMA 90.00 115.90 90.00
>       PERIODIC XYZ
>     &END CELL
>
>     &COORD
>  C         9.510000        3.334000        5.417000
>  C        10.770000        3.348000        4.827000
>  C        11.771000        2.497000        5.288000
>  C        11.518000        1.636000        6.343000
>  C        10.266000        1.639000        6.953000
>  C         9.279000        2.483000        6.489000
>  C         8.231000        4.763000        3.830000
>  C         6.944000        5.542000        3.720000
>  H        10.930000        3.957000        4.145000
>  H        12.675000        2.557000        4.918000
>  H        10.101000        1.062000        7.690000
>  H         8.407000        2.482000        6.891000
>  H        12.348000        0.517000        7.562000
>  H         7.724000        4.239000        5.582000
>  H         6.614000        5.480000        2.836000
>  H         6.512000        5.574000        4.484000
>  H         7.181000        6.589000        3.692000
>  N         8.426000        4.170000        5.017000
>  O        12.536000        0.800000        6.745000
>  O         9.035000        4.678000        2.901000
>  C         6.784000        8.034000        0.970000
>  C         5.524000        8.048000        1.560000
>  C         4.523000        7.197000        1.099000
>  C         4.776000        6.336000        0.044000
>  C         6.028000        6.339000       -0.567000
>  C         7.015000        7.183000       -0.102000
>  C         8.063000        9.463000        2.557000
>  C         9.350000       10.242000        2.667000
>  H         5.364000        8.657000        2.242000
>  H         3.618000        7.257000        1.469000
>  H         6.193000        5.762000       -1.303000
>  H         7.887000        7.182000       -0.505000
>  H         3.945000        5.217000       -1.175000
>  H         8.570000        8.939000        0.805000
>  H         9.680000       10.180000        3.551000
>  H         9.782000       10.274000        1.903000
>  H         9.113000       11.289000        2.695000
>  N         7.867000        8.870000        1.370000
>  O         3.758000        5.500000       -0.358000
>  O         7.259000        9.378000        3.486000
>  C         0.319000        6.066000        0.970000
>  C        -0.941000        6.052000        1.560000
>  C        -1.942000        6.903000        1.099000
>  C        -1.689000        7.764000        0.044000
>  C        -0.437000        7.761000       -0.567000
>  C         0.550000        6.917000       -0.102000
>  C         1.598000        4.637000        2.557000
>  C         2.885000        3.858000        2.667000
>  H        -1.101000        5.443000        2.242000
>  H        -2.847000        6.843000        1.469000
>  H        -0.272000        8.338000       -1.303000
>  H         1.422000        6.918000       -0.505000
>  H        -2.520000        8.883000       -1.175000
>  H         2.105000        5.161000        0.805000
>  H         3.215000        3.920000        3.551000
>  H         3.317000        3.826000        1.903000
>  H         2.648000        2.811000        2.695000
>  N         1.402000        5.230000        1.370000
>  O        -2.707000        8.600000       -0.358000
>  O         0.794000        4.722000        3.486000
>  C         3.045000        1.366000        5.417000
>  C         4.305000        1.352000        4.827000
>  C         5.306000        2.203000        5.288000
>  C         5.053000        3.064000        6.343000
>  C         3.801000        3.061000        6.953000
>  C         2.814000        2.217000        6.489000
>  C         1.766000       -0.063000        3.830000
>  C         0.479000       -0.842000        3.720000
>  H         4.465000        0.743000        4.145000
>  H         6.210000        2.143000        4.918000
>  H         3.636000        3.638000        7.690000
>  H         1.942000        2.218000        6.891000
>  H         5.883000        4.183000        7.562000
>  H         1.259000        0.461000        5.582000
>  H         0.149000       -0.780000        2.836000
>  H         0.047000       -0.874000        4.484000
>  H         0.716000       -1.889000        3.692000
>  N         1.961000        0.530000        5.017000
>  O         6.071000        3.900000        6.745000
>  O         2.570000        0.022000        2.901000
>     &END COORD
>
>
>     &KIND H
>       BASIS_SET 6-31++Gxx
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>
>     &KIND C
>       BASIS_SET 6-31++Gxx
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>
>     &KIND N
>       BASIS_SET 6-31++Gxx
>       POTENTIAL GTH-PBE-q5
>     &END KIND
>
>     &KIND O
>       BASIS_SET 6-31++Gxx
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>
>   &END SUBSYS
>
>   &PROPERTIES
>     &RESP
>       &PERIODIC_SYS
>         ATOM_LIST 1..80
> LENGTH 3.0
> RANGE  3.0 5.0
> SURF_DIRECTION Z
>       &END PERIODIC_SYS
>       &PRINT
> &V_RESP_CUBE
> &END V_RESP_CUBE
> &RESP_CHARGES_TO_FILE
> &END RESP_CHARGES_TO_FILE
> &PROGRAM_RUN_INFO
> &END
> &COORD_FIT_POINTS
> &END
>       &END PRINT
>
>     &END RESP
>
>     &FIT_CHARGE
>     &END FIT_CHARGE
>
>   &END PROPERTIES
>
> &END FORCE_EVAL
>
>
>
>
> RESP charges:
>   Type |   Atom   |    Charge
>
>   RESP       1  C     0.070078
>   RESP       2  C     0.903292
>   RESP       3  C     1.113722
>   RESP       4  C    -0.120125
>   RESP       5  C     1.058323
>   RESP       6  C     0.655164
>   RESP       7  C     0.200902
>   RESP       8  C     2.666416
>   RESP       9  H    -1.222912
>   RESP      10  H    -1.170830
>   RESP      11  H    -0.983979
>   RESP      12  H    -0.818745
>   RESP      13  H    -1.214944
>   RESP      14  H    -1.366249
>   RESP      15  H    -1.224385
>   RESP      16  H    -1.119378
>   RESP      17  H    -1.137280
>   RESP      18  N     1.259042
>   RESP      19  O     1.713353
>   RESP      20  O     0.738109
>   RESP      21  C     0.041413
>   RESP      22  C     0.956097
>   RESP      23  C     1.040182
>   RESP      24  C    -0.082712
>   RESP      25  C     1.051482
>   RESP      26  C     0.595410
>   RESP      27  C     0.202160
>   RESP      28  C     2.662283
>   RESP      29  H    -1.166123
>   RESP      30  H    -1.126516
>   RESP      31  H    -0.984189
>   RESP      32  H    -0.800838
>   RESP      33  H    -1.188989
>   RESP      34  H    -1.401436
>   RESP      35  H    -1.215709
>   RESP      36  H    -1.113423
>   RESP      37  H    -1.128041
>   RESP      38  N     1.271056
>   RESP      39  O     1.679915
>   RESP      40  O     0.705805
>   RESP      41  C     0.116651
>   RESP      42  C     0.813652
>   RESP      43  C     1.108160
>   RESP      44  C    -0.087035
>   RESP      45  C     1.066794
>   RESP      46  C     0.598212
>   RESP      47  C     0.201601
>   RESP      48  C     2.665972
>   RESP      49  H    -1.193708
>   RESP      50  H    -1.119339
>   RESP      51  H    -0.987625
>   RESP      52  H    -0.794927
>   RESP      53  H    -1.193920
>   RESP      54  H    -1.403616
>   RESP      55  H    -1.227170
>   RESP      56  H    -1.113105
>   RESP      57  H    -1.132964
>   RESP      58  N     1.272201
>   RESP      59  O     1.669491
>   RESP      60  O     0.737908
>   RESP      61  C     0.017005
>   RESP      62  C     0.961044
>   RESP      63  C     1.064429
>   RESP      64  C    -0.116028
>   RESP      65  C     1.044203
>   RESP      66  C     0.665757
>   RESP      67  C     0.203199
>   RESP      68  C     2.660164
>   RESP      69  H    -1.159143
>   RESP      70  H    -1.166104
>   RESP      71  H    -0.983609
>   RESP      72  H    -0.830205
>   RESP      73  H    -1.208912
>   RESP      74  H    -1.380887
>   RESP      75  H    -1.210223
>   RESP      76  H    -1.114933
>   RESP      77  H    -1.129467
>   RESP      78  N     1.264612
>   RESP      79  O     1.718065
>   RESP      80  O     0.706396
>   Total               0.000000
>
>
>  DDAP FULL DENSITY charges:
>   Atom     |    Charge
>
>      1  C     0.164768
>      2  C     0.038789
>      3  C    -0.067304
>      4  C     0.359095
>      5  C    -0.273509
>      6  C    -0.132861
>      7  C     0.453357
>      8  C    -0.073176
>      9  H    -0.008341
>     10  H    -0.007149
>     11  H     0.160840
>     12  H     0.127025
>     13  H     0.128967
>     14  H     0.094082
>     15  H    -0.056650
>     16  H    -0.027392
>     17  H    -0.004180
>     18  N    -0.249484
>     19  O    -0.299466
>     20  O    -0.327283
>     21  C     0.164803
>     22  C     0.039171
>     23  C    -0.067954
>     24  C     0.359126
>     25  C    -0.273851
>     26  C    -0.132660
>     27  C     0.453316
>     28  C    -0.072910
>     29  H    -0.008512
>     30  H    -0.006834
>     31  H     0.161121
>     32  H     0.126815
>     33  H     0.128910
>     34  H     0.094007
>     35  H    -0.056723
>     36  H    -0.027522
>     37  H    -0.004288
>     38  N    -0.249623
>     39  O    -0.299372
>     40  O    -0.327146
>     41  C     0.164786
>     42  C     0.039184
>     43  C    -0.067967
>     44  C     0.359125
>     45  C    -0.273855
>     46  C    -0.132651
>     47  C     0.453282
>     48  C    -0.072882
>     49  H    -0.008520
>     50  H    -0.006829
>     51  H     0.161118
>     52  H     0.126809
>     53  H     0.128911
>     54  H     0.094000
>     55  H    -0.056734
>     56  H    -0.027529
>     57  H    -0.004294
>     58  N    -0.249597
>     59  O    -0.299364
>     60  O    -0.327128
>     61  C     0.164787
>     62  C     0.038773
>     63  C    -0.067297
>     64  C     0.359102
>     65  C    -0.273505
>     66  C    -0.132867
>     67  C     0.453392
>     68  C    -0.073203
>     69  H    -0.008330
>     70  H    -0.007154
>     71  H     0.160838
>     72  H     0.127032
>     73  H     0.128964
>     74  H     0.094090
>     75  H    -0.056640
>     76  H    -0.027383
>     77  H    -0.004176
>     78  N    -0.249513
>     79  O    -0.299471
>     80  O    -0.327306
>   Total       0.000000
>
>
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