coordination number as a collective variable

sonali bankura bson... at gmail.com
Wed Dec 1 21:30:44 CET 2010


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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