[CP2K:5018] Periodic RESP charges for paracetamol form I crystal
mbellucci
mbell... at gmail.com
Mon Mar 3 21:56:18 UTC 2014
Thank you Dorothea and Juerg for your helpful comments. I managed to get
physically meaningful charges from the RESP fit by using restraints in the
RESP fit and using the DDAP charges as the target values. At the moment I
am varying the strength of the restraints in an effort to minimize the RMSD
of the fit. Thank you for your help!
Best,
Mike
On Monday, March 3, 2014 3:33:14 AM UTC-5, jgh wrote:
>
> 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<javascript:>
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com <javascript:> wrote: -----
> To: cp... at googlegroups.com <javascript:>
> From: mbellucci
> Sent by: cp... at googlegroups.com <javascript:>
> Date: 03/02/2014 08:36PM
> Cc: dorot... at googlemail.com <javascript:>
> 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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