[CP2K:5018] Periodic RESP charges for paracetamol form I crystal

hut... at chem.uzh.ch hut... at chem.uzh.ch
Mon Mar 3 08:33:14 UTC 2014


Hi

please remember that ESP calculations work by fitting the
electrostatic field away from the charge distribution.
In a dense periodic system (closely packed crystal or a liquid)
there is no space without charge density and you cannot use
the normal method. 
The periodic ESP code in CP2K is targeted for open systems
(zeolites, MOFs) and surfaces.
For liquids we developed a method based on Wannier functions
back in the CPMD days (J. Chem. Phys. 121, 5133-5142 (2004)),
not implemented in CP2K).
A work around would be to use QM/MM and self-consistently
get the charges.

regards

Juerg Hutter

--------------------------------------------------------------
Juerg Hutter                         Phone : ++41 44 635 4491
Institut für Chemie                  FAX   : ++41 44 635 6838
Universität Zürich                   E-mail: hut... at chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------

-----cp... at googlegroups.com wrote: -----
To: cp... at googlegroups.com
From: mbellucci 
Sent by: cp... at googlegroups.com
Date: 03/02/2014 08:36PM
Cc: dorothe... at googlemail.com
Subject: Re: [CP2K:5018] Periodic RESP charges for paracetamol form I crystal





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>:
 

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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