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