reproduce the recipe

Francesco francesc... at gmail.com
Wed Jun 11 11:35:58 CEST 2008


I'm trying to set the hight and width of the gaussian-shaped potential
hills as in the Ensing et al. 's article (section III.A page 6679)

1) for the hight i've used the keyword  WW int the subshell __ROOT__
%MOTION%FREE_ENERGY%METADYN

2) but i cannot find the keyword for the width of the gaussian.

Thanks in advance for any suggestions
Francesco



On 28 Mag, 14:57, ilya <ily... at gmail.com> wrote:
> Hi.
>
> The constant k_a is __ROOT__%MOTION%FREE_ENERGY%METADYN%METAVAR
> %LAMBDA, I think.
>
> The wall is needed for your system not to get out of desired values of
> colvar.
> So you have to define colvar first.
>
> Here is my input when I played with this system. I hope it still
> works :-)
>
> &GLOBAL
>   PROJECT_NAME CH3Cl2
>   RUN_TYPE MD
>   PRINT_LEVEL LOW
> &END GLOBAL
> &FORCE_EVAL
>   METHOD QS
>   &DFT
>     CHARGE -1
>     &QS
>       METHOD PM6
>       &SE
>       &END SE
>     &END QS
>     &SCF
>       SCF_GUESS ATOMIC
>       &PRINT
>         &RESTART OFF
>         &END
>       &END
>     &END SCF
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 20.0 20.0 20.0
>       UNIT ANGSTROM
>       PERIODIC NONE
>     &END CELL
>     &COORD
> Cl   1.8857504258947901E+00    4.6206939630623257E-02
> 2.1531234462208859E+00
> C    1.5316945738973686E+00    6.5338888135881557E-01
> 4.5150645817723678E-01
> Cl  -1.4314278208899731E-01    1.5429427578017161E+00
> -2.4277629573370545E+00
> H    2.1708763005804328E+00    1.4925710551721185E+00
> 2.5533970085140567E-01
> H    1.6682666293247128E+00   -2.9735657839978469E-01
> -1.9548531375683331E-01
> H    4.6054493765634713E-01    9.2819246053392856E-01
> 4.1726581436562926E-01
>     &END
>     &VELOCITY
>      7.0958036064996686E-05    5.7615299325917293E-05
> -1.4154179473477034E-04
>     -1.0727156994188417E-04    1.1714159721139608E-04
> -3.7784397372553975E-04
>     -3.6621108925639071E-05   -1.0195225619868995E-04
> 2.8894612626773259E-04
>     -2.1230250490388399E-04    5.7266710636374009E-04
> 3.0278546783035168E-04
>      1.3772055771530359E-03   -4.5659067644109784E-04
> 1.3644193763516073E-04
>     -1.0943574811747203E-03    4.7492760295814294E-05
> -1.1213758035568233E-03
>     &END VELOCITY
>     &COLVAR
>         &DISTANCE
>             ATOMS 1 2
>         &END DISTANCE
>     &END
>     &COLVAR
>         &DISTANCE
>             ATOMS 2 3
>         &END DISTANCE
>     &END
>   &END SUBSYS
> &END FORCE_EVAL
> &MOTION
>   &MD
>     ENSEMBLE NVT
>     STEPS 200000
>     TIMESTEP 0.5
>     TEMPERATURE 300.0
>     &THERMOSTAT
>       TYPE CSVR
>       &CSVR
>         TIMECON 200.0
>       &END CSVR
>     &END THERMOSTAT
>   &END MD
>   &FREE_ENERGY
>     METHOD METADYN
>     &METADYN
>       DO_HILLS TRUE
>       LAGRANGE TRUE
>       WW 0.0005
>       TEMPERATURE 0.0
>       NT_HILLS 100
>       &METAVAR
>         MASS 200.0
>         LAMBDA 0.5
>         COLVAR 1
>         SCALE 0.5
>         &WALL
>             TYPE QUADRATIC
>             POSITION 10.0
>             &QUADRATIC
>                 K 0.1
>                 DIRECTION WALL_PLUS
>             &END
>         &END WALL
>       &END METAVAR
>       &METAVAR
>         MASS 200.0
>         LAMBDA 0.5
>         COLVAR 2
>         SCALE 0.5
>         &WALL
>             TYPE QUADRATIC
>             POSITION 10.0
>             &QUADRATIC
>                 K 0.1
>                 DIRECTION WALL_PLUS
>             &END
>         &END WALL
>       &END METAVAR
>       &PRINT
>         &COLVAR
>           FILENAME =colvar
>         &END COLVAR
>       &END PRINT
>     &END METADYN
>   &END FREE_ENERGY
>   &PRINT
>     &TRAJECTORY
>       &EACH
>         MD 20
>       &END
>     &END
>   &END
> &END MOTION
>
> On May 28, 1:06 pm, Francesco <francesc... at gmail.com> wrote:
>
> > Hi all,
>
> > I'm trying to reproduce, STEP by STEP the SN2 reaction of JPC-B 2005,
> > 109 6676-6687, "A
> >recipefor the computation of the free energy barrier and the lowest
> > free energy path of
> > concerted reactions".
>
> > I am trying to setup the 2nd and 3rd terms on the right of Eq. 4. No
> > problems to setup
> > the mass of the fictious particle (2nd term). How should I write the
> > force constant k_a
> > and the reference position for the 3rd term ?
> > Is the quadratic wall (K,POSITION) the right solution ?
>
> > thanks,
> > Francesco


More information about the CP2K-user mailing list