<div dir="ltr"><div> </div><div>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!</div><div> </div><div>Best,</div><div> </div><div>Mike</div> On Monday, March 3, 2014 3:33:14 AM UTC-5, jgh wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="BF0pMAbhaDQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">hut...@chem.uzh.ch</a> Winterthurerstrasse 190 CH-8057 Zürich, Switzerland --------------------------------------------------------------- -----<a href="javascript:" target="_blank" gdf-obfuscated-mailto="BF0pMAbhaDQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> wrote: ----- To: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="BF0pMAbhaDQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> From: mbellucci Sent by: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="BF0pMAbhaDQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> Date: 03/02/2014 08:36PM Cc: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="BF0pMAbhaDQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">dorot...@googlemail.com</a> 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: <a href="https://groups.google.com/forum/#!msg/cp2k/G3THGbvvIcU/CgGZxvtbGrsJ" target="_blank" onmousedown="this.href='https://groups.google.com/forum/#!msg/cp2k/G3THGbvvIcU/CgGZxvtbGrsJ';return true;" onclick="this.href='https://groups.google.com/forum/#!msg/cp2k/G3THGbvvIcU/CgGZxvtbGrsJ';return true;">https://groups.google.com/forum/#!msg/cp2k/G3THGbvvIcU/CgGZxvtbGrsJ</a> Kind regards, Dorothea 2014-03-01 21:02 GMT+01:00 mbellucci <<a>mbel...@gmail.com</a>>: 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 -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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