[CP2K:2961] coordination number as a collective variable

Teodoro Laino teodor... at gmail.com
Wed Dec 1 22:31:34 CET 2010


Dear Sonali,

our coordination variable is normalized by the number of atoms. In your case 2 oxygen atoms and all the ideal values are therefore divided by 2. There is no way to change this behavior, unless you implement a CV coordination not-normalized.
the 0.1 value is different from zero, probably due to the value of your rc in the coordination function.

Teo

On Dec 1, 2010, at 9:30 PM, sonali bankura wrote:

> Dear CP2K users,
> I am trying to perform the protonation and deprotonation of liquid formic acid  with the CP2K metadynamics method.
> I have used the formic acid oxygen coordination numbers as the collective variables. The chosen collective coordinates
> are the coordination numbers of the carboxyl oxygen atoms (two oxygen atom) to all other hydroxyl hydrogern [only the O-H hydrogen].
> Using these generalized coordinates, it should be, the nutral formic acid coordination number Co-h ~ 1, The protonated
> formic acid coordination number Co-h~2 and deprotonated (formate ion) formic acid coodination number Co-h~0. 
> But the coordination number are found different from its ideal value (less than 1). For the nutral formic acid  Co-h ~ 0.5,
> protonated formic acid coordination number Co-h~0.9 and deprotonated (formate ion) formic acid coodination number Co-h~.1 
> I have used R0=1.6 angstrom in the coordination function. How can I solve this problem?
> 
> This is my input file. 
> &GLOBAL
> PRINT_LEVEL LOW
> PROJECT FOH
> PROGRAM CP2K
> RUN_TYPE MD
> WALLTIME 43000
> &END GLOBAL
> 
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS 8000
> TIMESTEP 0.5
> TEMPERATURE 300.0
> &THERMOSTAT
> TYPE NOSE
> REGION MOLECULE
> &NOSE
> LENGTH 3
> YOSHIDA 3
> TIMECON 100
> MTS 2
> &END NOSE
> &END THERMOSTAT
> &PRINT
> &ENERGY
> &EACH
> MD 1
> &END EACH 
> FILENAME =FOH.ene
> &END ENERGY
> &END PRINT
> &END MD
> # DO METADYNAMICS EVERY 20 STEPS (10 fs) with 1.0 kcal/mol HEIGHT
> &FREE_ENERGY
> METHOD METADYN
> &METADYN
> DO_HILLS
> NT_HILLS 20
> WW 0.0016
> &METAVAR
> COLVAR 1
> SCALE 0.05
> &END METAVAR
> &PRINT
> &COLVAR
> FILENAME =colvar
> &EACH
> MD 20
> &END EACH
> &END COLVAR
> &HILLS
> FILENAME =hills
> &EACH
> MD 20
> &END EACH
> &END HILLS
> &END PRINT
> &END METADYN
> &END FREE_ENERGY
> &PRINT
> &TRAJECTORY SILENT
> &EACH 
> MD 10
> &END EACH
> FILENAME =FOH.dcd
> FORMAT DCD
> &END TRAJECTORY
> &VELOCITIES OFF
> &EACH 
> MD 10
> &END EACH
> FILENAME =FOH.vel
> &END VELOCITIES
> &FORCES OFF
> &EACH 
> MD 10
> &END EACH
> FILENAME =FOH.for
> &END FORCES
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &RESTART SILENT
> &EACH 
> MD 10
> &END EACH
> FILENAME =FOH.restart
> &END RESTART
> &END PRINT
> &END MOTION
> 
> &FORCE_EVAL
> METHOD QUICKSTEP
> &DFT
> BASIS_SET_FILE_NAME ./BASIS_SET
> POTENTIAL_FILE_NAME ./POTENTIAL
> CHARGE 0
> &SCF
> MAX_SCF 40
> EPS_SCF 1.0E-6
> SCF_GUESS RESTART
> &OUTER_SCF
> EPS_SCF 1.0E-6
> MAX_SCF 10
> &END OUTER_SCF
> &OT
> PRECONDITIONER FULL_ALL
> MINIMIZER DIIS
> N_DIIS 7
> &END OT
> &PRINT
> &RESTART
> &EACH 
> MD 10
> &END EACH
> FILENAME =RESTART
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END SCF
> &QS
> EPS_DEFAULT 1.0E-12
> EXTRAPOLATION ASPC
> EXTRAPOLATION_ORDER 3
> &END QS
> 
> &MGRID
> CUTOFF 280
> COMMENSURATE
> &END MGRID
> &POISSON
> # POISSON_SOLVER MT
> POISSON_SOLVER PERIODIC
> PERIODIC XYZ
> &END POISSON
> &XC
> &XC_GRID
> XC_SMOOTH_RHO NN10
> XC_DERIV SPLINE2_SMOOTH
> &END XC_GRID
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
> &SUBSYS
> &CELL
> ABC 12.60 12.60 12.60
> PERIODIC XYZ
> &END CELL
> &COORD
> O 6.459781 8.056508 6.296098
> C 7.163456 7.125041 6.732669
> H 8.182514 7.323334 7.066482
> O 6.770119 5.821413 6.822736
> H 5.718549 5.683926 6.697456
> O 6.909952 2.509184 6.347867
> C 7.896109 2.851522 5.707026
> H 8.661729 2.175128 5.302803
> O 8.236772 4.119331 5.434266
> H 7.643341 4.773784 5.856131
> O 4.124040 4.748510 6.367797
> C 3.826171 4.079831 7.413561
> H 2.911557 4.162765 8.057558
> O 4.702719 3.252897 7.940200
> H 5.495648 3.098516 7.276470
> O 7.083500 0.801447 10.623640
> C 7.196982 1.634820 9.706008
> H 7.778468 1.371844 8.765636
> O 6.640886 2.809737 9.611978
> H 6.021287 2.908125 10.412297
> O 8.489833 2.288351 2.455063
> C 7.679999 1.503715 1.953385
> H 8.004016 0.575160 1.499982
> O 6.331616 1.743520 1.861442
> H 6.295148 2.780825 2.098260
> O 5.664177 -0.290593 5.373825
> C 5.056596 0.661018 4.942813
> H 5.121344 1.018664 3.844198
> O 4.048135 1.244555 5.708744
> H 3.943226 0.801882 6.633520
> O 7.351965 7.140197 3.238899
> C 7.307747 7.292219 1.957629
> H 6.386861 6.950826 1.436370
> O 8.327481 7.875422 1.353614
> H 9.120440 7.978032 2.056322
> O 6.106112 4.268650 2.299097
> C 5.799206 4.316004 3.548140
> H 5.556844 3.381579 4.156157
> O 5.770873 5.431324 4.260241
> H 6.278060 6.218091 3.789728
> O 3.084212 1.479342 1.755576
> C 3.258946 0.396132 1.125847
> H 2.508868 -0.427617 0.964556
> O 4.406919 0.180757 0.419176
> H 5.169578 0.758113 0.719269
> O 1.030561 0.825643 10.008227
> C 1.783958 1.802656 10.248734
> H 1.407950 2.761985 10.678268
> O 3.112659 1.847893 10.048674
> H 3.554449 1.216543 9.380070
> O 1.253780 8.870214 6.225453
> C 2.257224 9.397345 6.729775
> H 2.508456 9.461020 7.787119
> O 3.297263 9.862703 6.012998
> H 3.096095 9.917562 5.000798
> O 10.369401 8.316547 2.866836
> C 10.256690 8.249763 4.106692
> H 11.083242 8.538807 4.860478
> O 9.137828 7.985956 4.735631
> H 8.392881 7.628317 4.134091
> O 3.664910 8.385721 9.219956
> C 3.550214 7.189969 8.825279
> H 2.623363 6.887540 8.267633
> O 4.336981 6.125011 9.051637
> H 5.276801 6.492500 9.468660
> O 8.113374 10.054495 3.054541
> C 8.286448 10.528097 4.157214
> H 7.710155 10.320824 5.027996
> O 9.242023 11.434313 4.468067
> H 9.756812 11.726453 3.660706
> O 5.005743 3.012838 -0.012323
> C 4.081765 3.819001 -0.253009
> H 4.127414 4.654782 -0.914101
> O 2.967043 3.883029 0.461207
> H 3.039859 3.176162 1.154938
> O 10.165725 1.229098 7.008693
> C 11.367460 1.165506 6.562970
> H 11.958104 1.960840 6.127166
> O 12.027848 -0.013202 6.390440
> H 11.371208 -0.740315 6.692291
> O -0.577225 2.282373 0.646075
> C -1.509503 2.225770 -0.132934
> H -2.561031 2.545444 0.052443
> O -1.456205 1.662727 -1.378040
> H -0.442135 1.330523 -1.489236
> O 10.555040 10.968234 0.593169
> C 9.888683 10.093122 0.035767
> H 9.998981 9.004327 0.174939
> O 8.964099 10.379899 -0.924083
> H 8.565263 11.297233 -0.849804
> O 3.094378 3.894949 3.453685
> C 2.021610 3.445151 3.836126
> H 1.122624 3.749433 3.311372
> O 1.893391 2.434526 4.709074
> H 2.763960 1.996969 4.955929
> O 12.020802 6.427450 8.220920
> C 11.180152 7.342253 7.997811
> H 11.525702 8.056501 7.226946
> O 9.987535 7.436066 8.557799
> H 9.950028 6.658945 9.303061
> O 9.629528 5.870730 10.381703
> C 8.465271 5.367125 10.270255
> H 7.920763 5.583338 9.386205
> O 7.791088 4.762825 11.277155
> H 8.324699 4.746763 12.211556
> O 4.045846 7.058285 0.448421
> C 3.246323 6.761549 1.412440
> H 3.356992 5.865156 2.077310
> O 2.183205 7.514649 1.741086
> H 1.976016 8.233811 1.062838
> O -0.451564 12.476867 3.249723
> C 0.566046 11.747444 3.399303
> H 1.397718 11.965692 4.095191
> O 0.695218 10.573921 2.704840
> H -0.053107 10.576586 2.007093
> O 9.430169 5.225144 1.778048
> C 10.237226 5.055058 2.698643
> H 10.612823 5.903150 3.198559
> O 10.855284 3.912604 2.999382
> H 10.529005 3.202497 2.361735
> O 0.846705 3.461511 8.238902
> C -0.265138 3.819748 7.859488
> H -1.132885 3.533797 8.471083
> O -0.557023 4.409714 6.672273
> H 0.226207 4.844563 6.169906
> O 6.434192 7.355910 9.595535
> C 6.480993 8.513487 10.088883
> H 7.201953 9.328683 9.902081
> O 5.629369 8.917621 11.020820
> H 4.860280 8.266977 11.197220
> O 10.320602 -1.683661 7.327907
> C 9.149270 -1.608931 7.760573
> H 8.590673 -2.490773 8.186227
> O 8.443110 -0.475193 7.935741
> H 9.168722 0.226790 7.666053
> O 3.835103 10.431785 3.477700
> C 4.705925 9.685083 2.972356
> H 5.352604 10.006369 2.152012
> O 5.046082 8.433438 3.400453
> H 4.462333 8.127420 4.144083
> O 2.098257 9.312925 -0.191389
> C 1.380951 9.650267 -1.202713
> H 1.663358 10.483579 -1.757955
> O 0.226948 9.120008 -1.541336
> H 0.138752 8.172229 -1.133408
> O 4.106698 11.990078 8.211988
> C 4.870600 11.082915 8.660361
> H 4.793638 10.787877 9.754473
> O 5.595374 10.290161 7.911755
> H 5.358137 10.538576 6.923987
> O 0.882067 5.860265 4.738442
> C 1.727164 6.738016 4.539868
> H 1.438878 7.659225 4.038307
> O 3.044999 6.761288 4.882832
> H 3.349001 5.950273 5.432134
> O 0.102684 7.049788 11.618558
> C 0.730715 5.954988 11.473636
> H 0.699110 5.214057 12.217627
> O 1.387672 5.606141 10.400733
> H 1.013165 5.950356 9.473770
> &END COORD
> &COLVAR
> &COORDINATION
> ATOMS_FROM 1 4
> ATOMS_TO 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
> ATOMS_TO 90 95 100 105 110 115 120 125 130 135 140 145 150 155 160
> R_0 [angstrom] 1.6
> NN 6
> ND 18
> &END COORDINATION
> &END COLVAR
> &KIND H
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND C
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q4
> &END KIND
> &KIND O
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &PRINT
> &MOLECULES
> &END MOLECULES
> &END PRINT
> &END SUBSYS
> &END FORCE_EVAL
> 
> This is my HILLS file
> 10.0 0.54429 0.05000 0.00160
> 20.0 0.52151 0.05000 0.00160
> 30.0 0.50277 0.05000 0.00160
> 40.0 0.49177 0.05000 0.00160
> 50.0 0.48283 0.05000 0.00160
> 60.0 0.48205 0.05000 0.00160
> 70.0 0.48504 0.05000 0.00160
> 80.0 0.48519 0.05000 0.00160
> 90.0 0.48598 0.05000 0.00160
> 100.0 0.48460 0.05000 0.00160
> 110.0 0.47717 0.05000 0.00160
> 120.0 0.46886 0.05000 0.00160
> 130.0 0.46423 0.05000 0.00160
> 140.0 0.47542 0.05000 0.00160
> 150.0 0.48298 0.05000 0.00160
> 160.0 0.47676 0.05000 0.00160
> 170.0 0.45979 0.05000 0.00160
> 180.0 0.48752 0.05000 0.00160
> 190.0 0.46446 0.05000 0.00160
> 200.0 0.49344 0.05000 0.00160
> 210.0 0.57036 0.05000 0.00160
> 220.0 0.64062 0.05000 0.00160
> 230.0 0.76264 0.05000 0.00160
> 240.0 0.84557 0.05000 0.00160
> 250.0 0.66548 0.05000 0.00160
> 260.0 0.67990 0.05000 0.00160
> 270.0 0.63364 0.05000 0.00160
> 280.0 0.59721 0.05000 0.00160
> 290.0 0.55210 0.05000 0.00160
> 300.0 0.57908 0.05000 0.00160
> 310.0 0.70571 0.05000 0.00160
> 320.0 0.84142 0.05000 0.00160
> 330.0 0.78512 0.05000 0.00160
> 340.0 0.68261 0.05000 0.00160
> 350.0 0.64575 0.05000 0.00160
> 360.0 0.61974 0.05000 0.00160
> 370.0 0.59782 0.05000 0.00160
> 380.0 0.63271 0.05000 0.00160
> 390.0 0.69847 0.05000 0.00160
> -------------------------------------------
> -------------------------------------------
> Thanks
> Sonali
> 
> 
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