Puzzled by QM/MM Error
Ali
rnalo... at gmail.com
Tue Nov 23 17:47:45 UTC 2010
Dear CP2K users,
I am attempting to set up a QM/MM calculation that consists of two
thymine bases solvated by 32 quantum waters and then surrounded by
classical waters. The thymines and the 32 waters are the QM part and
make a total of 128 atoms. The only classical empirical interactions
are the O-O of the classical waters which are treated with LJ
interactions.
I seem to be getting a rather puzzling error asking for the charges of
the Carbons and Nitrogens of the thymines that are treated with QM and
are defined with QM_KIND and thus shouldn't have any charges. The
error is shown below along with my input file. Any pointers would be
greatly appreciated:
&FORCE_EVAL
METHOD QMMM
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
COMMENSURATE
CUTOFF 300
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
EPS_GVG 1.0E-6
EPS_PGF_ORB 1.0E-6
EXTRAPOLATION PS
EXTRAPOLATION_ORDER 2
MAP_CONSISTENT
&END QS
&SCF
SCF_GUESS atomic
&END SCF
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&END DFT
&MM
&FORCEFIELD
&BEND
ATOMS H O H
K 0.
THETA0 1.8
&END BEND
&BOND
ATOMS O H
K 0.
R0 1.8
&END BOND
&CHARGE
ATOM O
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM H
CHARGE 0.4238
&END CHARGE
&NONBONDED
&LENNARD-JONES
atoms O O
EPSILON 78.198
SIGMA 3.166
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms O H
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms H H
EPSILON 0.0
SIGMA 3.30523
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms C H
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms N H
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms N N
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms C C
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms C O
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&LENNARD-JONES
atoms C N
EPSILON 0.0
SIGMA 3.6705
RCUT 11.4
&END LENNARD-JONES
&END NONBONDED
&SPLINE
EMAX_SPLINE 1.0
RCUT_NB 10.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE ewald
ALPHA .44
GMAX 21
&END EWALD
&END POISSON
&END MM
&QMMM
USE_GEEP_LIB 9
NOCENTER TRUE
NOCENTER0 TRUE
&CELL
ABC 13.0 13.0 13.0
&END CELL
ECOUPL GAUSS
&PERIODIC
GMAX=0.5
&MULTIPOLE
EWALD_PRECISION 1.0E-6
&END MULTIPOLE
&END PERIODIC
NOCOMPATIBILITY
&INTERPOLATOR
EPS_R 1.0e-14
EPS_X 1.0e-14
MAXITER 100
&END INTERPOLATOR
&WALLS
TYPE REFLECTIVE
WALL_SKIN 1.0
&END WALLS
&QM_KIND H
MM_INDEX 1 12 21 22 23 24 25 26 27 28 29 30
MM_INDEX 32 33 35 36 38 39 41 42 44 45 47 48
MM_INDEX 50 51 53 54 56 57 59 60 62 63 65 66
MM_INDEX 68 69 71 72 74 75 77 78 80 81 83 84 86 87
MM_INDEX 89 90 92 93 95 96 98 99 101 102 104 105
MM_INDEX 107 108 110 111 113 114 116 117 119 120
MM_INDEX 122 123 125 126
&END QM_KIND
&QM_KIND O
MM_INDEX 4 7 10 15
MM_INDEX 31 34 37 40 43 46 49 52 55 58
MM_INDEX 61 64 67 70 73 76 79 82 85 88 91
MM_INDEX 94 97 100 103 106 109 112 115 118
MM_INDEX 121 124
&END QM_KIND
&QM_KIND N
MM_INDEX 2 5 13 16
&END QM_KIND
&QM_KIND C
MM_INDEX 3 6 8 9 11 14 17 18 19 20
&END QM_KIND
#
# QM_KINDS
#
#
# MM_KINDS
#
#
&END QMMM
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
&END CELL
&COORD
H 1.3265234345 -1.8865675723 -2.0512810579
N 1.5084965848 -1.0085192834 -1.5224805373
C 2.8793594817 -0.6633359876 -1.4041525821
O 3.8272162517 -1.3649740635 -1.8073631633
N 3.1440393260 0.6068944606 -0.8158383642
C 2.2642571358 1.3967775816 -0.0901778198
O 2.6410987746 2.3871311909 0.5863796238
C 0.7793138032 1.1750739374 -0.3895977323
C 0.3814022015 2.4325806330 -1.1612154997
O -0.1881629203 0.9185593108 0.7287113772
C 0.4043218940 -0.1600225668 -1.0728654040
H -2.1155602468 -3.1284713253 2.6826176774
N -1.6142233083 -2.5953380784 1.9442117947
C -0.2279865556 -2.4177885739 1.9604698721
O 0.6169801467 -3.1123915877 2.6782587628
N 0.2872656433 -1.4667058888 1.1563230628
C -0.3446621049 -0.5357940079 0.3056375573
C -1.8439884528 -0.8284670449 0.3151745888
C -2.8018644226 -0.0371198599 -0.5384776143
C -2.3926457605 -1.7323234589 1.1534525768
H -0.4011257202 -0.0510960289 -1.8809852618
H 4.0716052966 1.1305331515 -1.0657791408
H 1.2176170933 -1.1818834456 1.4783854814
H -3.5171130836 -1.8144284240 1.2591701451
H 1.0884830434 2.6038476319 -2.0074660678
H 0.4619897117 3.2549893462 -0.4707652729
H -0.5480814835 2.3973199315 -1.6592412651
H -2.5182026709 1.0150972872 -0.7364425472
H -3.7943756756 -0.2080832655 -0.0525163232
H -2.9140737161 -0.5385619101 -1.5358351590
O 23.0194301600 6.9565529820 0.7100297213
H 23.1576004000 6.3303451540 1.4773449900
H 23.9050502800 7.1986222270 0.3136827052
O 9.5895214080 10.1607704200 -12.8462400400
H 9.4776334760 10.8078098300 -13.6004400300
H 8.7030105590 9.7582225800 -12.6180896800
O 19.9108505200 10.0517301600 10.0436000800
H 19.0872707400 9.5023889540 9.9024381640
H 20.0470295000 10.2027902600 11.0227003100
O 0.4929814935 -12.5368003800 -28.7772903400
H -0.4542287886 -12.2203702900 -28.7256298100
H 1.0653860570 -11.8136797000 -29.1638793900
O 23.2148208600 -3.7521169190 -4.5298910140
H 23.4040508300 -4.3824429510 -3.7769749160
H 22.9440403000 -2.8632099630 -4.1603989600
O 18.4907093000 9.1452198030 -9.9954853060
H 17.9631004300 8.5504293440 -10.6020002400
H 18.9171905500 8.5951738360 -9.2774600980
O 1.7868080140 -8.0634737010 -25.9675102200
H 1.4989420180 -8.9740381240 -26.2641696900
H 2.6609160900 -7.8342161180 -26.3957405100
O -14.3675499000 11.0813598600 -10.3355197900
H -14.6070995300 10.2516298300 -9.8313779830
H -14.4350900700 10.9058504100 -11.3176803600
O 21.8172702800 2.6671450140 -12.5647296900
H 20.9549598700 2.5602331160 -12.0697603200
H 21.6598491700 2.5282258990 -13.5424404100
O -4.7438168530 15.9610300100 -19.2812595400
H -3.8322689530 16.3491706800 -19.4170093500
H -4.6626858710 15.0626001400 -18.8497009300
O 10.6268301000 -4.1513209340 -14.0740699800
H 11.0991697300 -4.4050879480 -14.9181604400
H 9.6704683300 -4.4384818080 -14.1279897700
O 11.2847700100 12.4483003600 -14.5076198600
H 10.9997100800 13.0066700000 -15.2867002500
H 10.9614896800 12.8689899400 -13.6599702800
O 20.1488208800 3.7053558830 -7.5548968320
H 19.5200996400 4.0239810940 -6.8455400470
H 20.0364799500 2.7198109630 -7.6817059520
O 16.4992103600 -7.9503750800 -4.2549519540
H 16.3759193400 -8.9427385330 -4.2514138220
H 16.4455795300 -7.6044621470 -3.3182199000
O 12.9551401100 29.1213207200 6.6496877670
H 12.7815504100 28.1908893600 6.3269557950
H 13.1089496600 29.7228107500 5.8657522200
O 1.0678910020 -3.4366979600 -18.1886196100
H 1.0045839550 -2.7987310890 -17.4211597400
H 1.9897030590 -3.8225069050 -18.2262191800
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H -19.1859493300 8.8909034730 -7.9342370030
O -12.2898798000 11.1413297700 8.4484376910
H -11.3868999500 11.4740104700 8.1764860150
H -12.5524902300 11.5619897800 9.3168182370
O 14.0246000300 -1.4509539600 -20.1588497200
H 14.8587598800 -1.9993970390 -20.2170105000
H 13.8195200000 -1.0599219800 -21.0560894000
O 34.0571594200 -1.8328839540 4.9691410060
H 34.5174789400 -2.7204279900 4.9884328840
H 33.6293792700 -1.6598880290 5.8563117980
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H -2.6242609020 16.2473297100 -2.6259319780
O -5.8620672230 16.7971897100 -13.1794395400
H -6.5883421900 16.7628002200 -12.4928998900
H -5.3026528360 17.6129207600 -13.0323295600
O 7.6257410050 -13.2655201000 -3.2168929580
H 7.9813671110 -13.3384504300 -2.2851150040
H 7.6277441980 -14.1687202500 -3.6461029050
O 6.7048420910 0.8662474751 -2.7678411010
H 7.0068540570 1.3836090560 -1.9671369790
H 7.4253802300 0.8744143248 -3.4612081050
O -9.7479763030 30.3922100100 2.6262650490
H -9.7087326050 30.1485195200 1.6572070120
H -9.4306545260 31.3328704800 2.7465510370
O 23.1483802800 -7.0884361270 0.2011833042
H 23.1158695200 -7.9629240040 -0.2827737927
H 23.9245700800 -7.0850300790 0.8316708803
O 7.0429410930 29.0211200700 -7.5834980010
H 7.1002540590 29.5701293900 -6.7496500020
H 7.9617271420 28.7419796000 -7.8626260760
O -17.9281806900 2.2177250390 9.0142869950
H -17.1885795600 2.5704689030 9.5874948500
H -17.5462703700 1.8493369820 8.1666793820
O 2.5521090030 -23.7844505300 -4.5328569410
H 2.4512710570 -23.2271099100 -3.7087180610
H 3.0481860640 -24.6234397900 -4.3092508320
O -4.0679440500 3.7516069410 4.6600837710
H -4.4881119730 3.9991450310 3.7870519160
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O 0.0973890424 -12.2637701000 17.5827503200
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H -13.5572300000 28.4313392600 -22.7693691300
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H -2.0055739880 -2.9085938930 -17.8558406800
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H 9.2298049930 13.6788101200 -9.7140321730
H 10.5397396100 12.7475299800 -10.0029802300
O 22.4781093600 7.1412758830 5.3809599880
H 23.3434505500 7.5057411190 5.0369319920
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O 13.6625604600 -2.0565359590 -2.0677959920
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H 13.1016101800 -2.2867350580 -1.2725930210
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H 13.3608503300 22.1254596700 -18.8151893600
H 12.1637401600 21.0149402600 -18.7961692800
O 3.7648398880 9.2906484600 1.4958579540
H 3.4514160160 8.4253139500 1.1047530170
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H 4.8169112210 16.2348194100 -11.9717197400
H 3.2622580530 15.9273901000 -11.5777301800
O 7.0591268540 -2.5424239640 -3.6502819060
H 6.8208351140 -2.4341559410 -2.6851420400
H 7.9751691820 -2.1748340130 -3.8107318880
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H -3.9433031080 11.4449901600 2.0924589630
H -3.7542989250 13.0622396500 2.2167160510
O 10.7747297300 -17.6721401200 4.9310011860
H 11.6490001700 -18.1015491500 4.7045989040
H 10.3974504500 -17.2338695500 4.1151738170
O 4.0623669620 17.9076404600 -8.3104686740
H 3.7613101010 17.0050792700 -8.0026388170
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O 16.6888008100 -7.1364130970 18.2093696600
H 15.8145799600 -6.6669278140 18.0855503100
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O 22.7388305700 -0.6516780257 -13.0891704600
H 22.4906292000 -1.5163509850 -13.5259103800
H 23.2672901200 -0.8363813162 -12.2605495500
O 11.6723604200 4.8914017680 13.1567201600
H 12.3018598600 5.3656902310 13.7721796000
H 11.6977195700 5.3242349620 12.2556104700
O 8.9860706330 -1.0045900340 -13.7406902300
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H 5.3057780270 -18.8506507900 -13.2354297600
H 5.2918829920 -19.5500106800 -14.7110300100
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H 1.3815239670 17.6738205000 -9.6114711760
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O 24.0145607000 -5.6277470590 -17.0488300300
H 23.0175705000 -5.5504131320 -17.0435199700
H 24.3902797700 -5.0449810030 -17.7693996400
O 14.7568798100 -19.4245090500 -6.6554369930
H 14.1749095900 -20.1721897100 -6.3356280330
H 15.0058097800 -18.8415908800 -5.8819742200
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H 0.5460398793 4.2511482240 -4.6510620120
H -0.4033901095 3.3047339920 -5.5835709570
O 9.6394472120 -0.7285053134 7.8860220910
H 10.6067400000 -0.8555225730 8.1056118010
H 9.0794363020 -1.2339659930 8.5424509050
O 15.9884595900 -25.2151203200 -2.2969720360
H 16.3503093700 -25.0289001500 -1.3835229870
H 15.1254901900 -25.7142105100 -2.2183051110
O -3.7357380390 -15.0003204300 7.1933841710
H -4.0373301510 -15.1072397200 8.1408071520
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H -14.9663801200 -18.2673091900 6.3459081650
O 1.5865789650 -9.2064018250 3.5431001190
H 2.5227119920 -8.9308118820 3.3246870040
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H -17.8640594500 -17.0262699100 15.1528701800
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O -17.5270099600 -16.0724296600 0.0976934880
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H -17.5600490600 -16.7414703400 0.8401911855
O -2.0851640700 15.0559301400 7.4404778480
H -2.0298631190 15.6784496300 6.6598258020
H -2.2242109780 14.1215295800 7.1125168800
O -7.8666110040 -5.6659898760 9.1669692990
H -7.1695280080 -6.3733630180 9.0499267580
H -8.5836477280 -5.7877969740 8.4806604390
O 6.6440057750 -21.2722091700 -3.5834360120
H 6.6073269840 -22.2714290600 -3.5686149600
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O 13.6542596800 -21.9861602800 -2.6183159350
H 13.6585302400 -21.0019207000 -2.7950830460
H 13.9235801700 -22.1557598100 -1.6703170540
O 12.4520301800 -18.9220409400 35.7312088000
H 12.8399601000 -18.0118503600 35.5860710100
H 12.0468196900 -19.2515602100 34.8784408600
O -2.2976469990 -18.1440391500 8.5728645320
H -1.7380889650 -18.9583301500 8.7272367480
H -1.9723550080 -17.4004097000 9.1569767000
O -16.7045192700 10.6485099800 -15.6783304200
H -16.9085102100 11.5052299500 -15.2046098700
H -16.9849300400 9.8769226070 -15.1073398600
O 20.4205799100 -5.0254569050 -4.9492912290
H 20.5579204600 -5.8123607640 -5.5508880620
H 21.1637496900 -4.3698649410 -5.0830588340
O -11.6516895300 8.3909378050 9.5621166230
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O -8.6500759120 -29.9696292900 11.7331399900
H -9.2449588780 -30.6951198600 12.0792303100
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O -16.4578208900 -8.4988241200 22.6464004500
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O 20.1590900400 4.5010881420 2.2067999840
H 20.7408294700 4.0854020120 1.5076659920
H 19.9115905800 5.4284701350 1.9262570140
O 2.6065270900 6.8923659320 -2.9442780020
H 2.4761760230 5.9024620060 -2.9999480250
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H 3.5873229500 -6.8173189160 12.3427496000
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O -9.4665517810 1.9827510120 6.8647241590
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O -17.7355594600 -11.0089597700 15.4733896300
H -17.8525905600 -12.0008697500 15.5225400900
H -17.6589298200 -10.6361103100 16.3981094400
O -3.0983068940 -18.2443504300 11.9612503100
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H -2.3144400120 -18.5965805100 11.4498901400
O -5.2873969080 -9.9227027890 -4.4297180180
H -5.3376889230 -9.9661464690 -3.4319291110
H -5.6241922380 -9.0344552990 -4.7421040530
O -12.0059299500 -3.0701360700 18.4063091300
H -12.0933704400 -3.8047699930 17.7335090600
H -11.0614099500 -3.0270259380 18.7319297800
O -7.6046080590 0.0878872424 0.1016326025
H -6.6866807940 0.0021529302 0.4890072048
H -7.9840059280 0.9823899269 0.3381100893
O -5.1799368860 -28.6134700800 13.3579301800
H -4.3882517810 -28.1182498900 13.7156896600
H -4.8687829970 -29.4139595000 12.8456897700
O -17.4173202500 -7.1520900730 -4.4010109900
H -17.0863494900 -7.8107190130 -3.7252399920
H -16.6415500600 -6.6551852230 -4.7899379730
O -23.4368400600 -16.5287704500 9.1883316040
H -24.3743190800 -16.1897792800 9.1095476150
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O -9.7906789780 21.1323890700 14.6171398200
H -8.8853940960 21.0908203100 15.0399103200
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O 9.2895202640 -16.6257896400 -1.6727470160
H 9.5844764710 -16.2166099500 -2.5362141130
H 8.6457424160 -16.0120201100 -1.2157560590
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H -7.5487871170 -9.6344728470 41.2776489300
H -7.8518958090 -8.0923986430 41.7212905900
O 4.0738878250 -9.2520389560 -6.5391750340
H 3.7838940620 -8.5548439030 -5.8835668560
H 3.2966630460 -9.8381156920 -6.7681617740
O -4.2555952070 -11.6509599700 6.1291689870
H -4.3324050900 -11.7707099900 7.1189961430
H -4.7553601260 -12.3823299400 5.6651301380
O 5.2833719250 -20.6982708000 8.9935846330
H 5.6560630800 -21.6233501400 8.9207029340
H 4.9871778490 -20.3861408200 8.0908966060
O -16.8476791400 -22.5359401700 -1.0479899640
H -16.1689491300 -23.2563400300 -0.9053251743
H -17.2852592500 -22.3129806500 -0.1768933982
O -0.2483122051 13.4936599700 2.2794389720
H -0.8330844045 13.5446100200 3.0890350340
H 0.4166569114 14.2402200700 2.3010230060
O -32.9757003800 -3.9035758970 1.1874899860
H -33.3324585000 -2.9979319570 1.4166870120
H -31.9944496200 -3.8391358850 1.0058490040
O -19.3528099100 -10.5602197600 3.8254010680
H -19.9270305600 -11.0631103500 4.4714407920
H -19.3917408000 -11.0034103400 2.9298219680
O -7.3917398450 -9.1227006910 24.3713302600
H -7.6824760440 -8.2456579210 23.9888801600
H -6.9479408260 -8.9705629350 25.2544498400
O 7.5740809440 -16.4692897800 -14.2126102400
H 7.2895369530 -16.5080604600 -13.2547302200
H 7.5809822080 -17.3928794900 -14.5959396400
O -14.8873596200 -13.2918901400 17.9399204300
H -14.5953903200 -12.3622798900 17.7149906200
H -15.8622398400 -13.2903995500 18.1626300800
O -6.5935940740 2.8130729200 -21.7168502800
H -6.1727190020 2.3397920130 -20.9429893500
H -5.9416627880 3.4656178950 -22.1030807500
O -12.4165897400 2.2186219690 12.7001199700
H -12.9323301300 3.0637669560 12.8406200400
H -11.4454603200 2.3890750410 12.8670301400
O -8.1421375270 13.6753702200 -4.7557959560
H -8.1646442410 12.8412399300 -5.3069071770
H -7.2204780580 14.0628900500 -4.7750959400
&END COORD
&KIND H
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PRINT_LEVEL MEDIUM
PROJECT wateroxetane
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
COMVEL_TOL 0.000005
ENSEMBLE NVT
STEPS 100
TIMESTEP 0.5
TEMPERATURE 300.0
! TEMP_TOL 50
! &PRINT
! &ENERGY
! EACH 5
! &END ENERGY
! &RESTART
! EACH 100
! &END RESTART
! &END PRINT
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 50.
&END CSVR
&END THERMOSTAT
&END MD
&END MOTION
Here is the error that I get:
" FORCEFIELD| WARNING: A non Critical ForceField parameter is missing!
CP2K GOES!
FORCEFIELD| Non critical parameters are:Urey-
Bradley,Torsions,Impropers and 1-4
FORCEFIELD| All missing parameters will not contribute to the
potential energy!
FORCEFIELD| Missing Charge
( N)
FORCEFIELD| Missing Charge
( C)
*
*** ERROR in release_FF_missing_par ***
*
*** Missing critical ForceField parameters! Abort.. ***
===== Routine Calling Stack =====
6 force_field_pack
5 force_field_control
4 fist_init
3 fist_create_force_env
2 qmmm_create_force_env
1 CP2K"
Ali
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