reproduce the recipe

[ilya]

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
> recipe for 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