[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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