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

mbellucci mbell... at gmail.com
Sun Mar 2 19:35:53 UTC 2014





Hi Dorothea,

Thanks for the reply.  I tried what you suggested, i.e. using the 
NONPERIODIC_SYS keyword instead of the PERIODIC_SYS keyword, but it only 
seems to give physically meaningful charges when I make the cell dimensions 
very large (25.0 25.0 25.0 cubic box) so that all 4 molecules that make up 
the unit cell are completely within the box.  However, these very large 
cubic cell dimensions don't correspond to the actual dimensions of the 
monoclinic unit cell, and so, the periodicity with this large cell doesn't 
correspond the periodicity of the actual crystal.  When I try to use the 
cell dimensions of the unit cell (see previously posted input file) with 
the NONPERIODIC_SYS keyword, once again I end up with non-physical RESP 
charges.  I've also tried a range of different values for RMIN and RMAX in 
the NONPERIODIC_SYS section, but this doesn't seem to help very much. 
 Perhaps I am missing something simple, and so any suggestions would be 
appreciated.

Mike


On Saturday, March 1, 2014 3:19:58 PM UTC-5, Dorothea Golze wrote:
>
> 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 <mbel... at gmail.com <javascript:>>:
>
>>
>> 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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