[CP2K:5015] Periodic RESP charges for paracetamol form I crystal
Dorothea Golze
dorothe... at googlemail.com
Sat Mar 1 20:42:42 UTC 2014
Hi Mike and Carlos
Yes, this problem is indeed taken care of. My implementation takes this
into account. It is working since version 2.4.
Regards,
Dorothea
2014-03-01 21:29 GMT+01:00 mbellucci <mbell... at gmail.com>:
>
> Hi Carlos,
>
> Thank you for your reply. I have seen your paper before and I saw that
> you mentioned it on another thread related to periodic RESP fitting. I am
> also not familiar with the inner workings of CP2K, but in the previous
> thread related to periodic RESP fitting, someone (Dorothea Golze) mentioned
> that the problem you identified in your paper is taken care of in the
> periodic RESP fit in the current version of CP2K. Based on the version
> history of CP2K, it appears the last time any changes related to the RESP
> fitting was made was in version 2.4. Since I'm using version 2.5 of CP2K,
> I'm assuming that it should work and the problem you mention is taken into
> account.
>
> Mike
>
>
> On Saturday, March 1, 2014 3:12:03 PM UTC-5, ccampana wrote:
>
>> *Hi,*
>> *I am not familiar with the CP2K inner workings but if you want to
>> understand the basis of why fitting ESP charges for periodic systems
>> requires extra care I recommend you read the paper below.*
>> *DOI: *10.1021/ct9003405
>> Carlos
>>
>>
>> On Sat, Mar 1, 2014 at 3:02 PM, mbellucci <mbel... at gmail.com> wrote:
>>
>>>
>>> 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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