Once again about periodic colvar

[ilya]

Here is the input with one of many parameter values for metadynamics
I've tried.
(Sorry, it's not as attachment. Google FAQs says that to attach a file
you have to send e-mail to group's address. How to make it to appear
here?)


&GLOBAL
  PROJECT_NAME BUTANE
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
  METHOD QS
  &DFT
    &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
C   -8.1866427536766317E-01   -9.8145723495914294E-01
-1.9509803466736661E-01
C   -5.8924914610730947E-02    2.3406403231329728E-01
3.6337090710811820E-01
C   -5.0164001189101215E-01    1.5910014193467945E+00
-2.8293078840561836E-01
C    4.9476299744407765E-01    2.6396358566826095E+00
1.2828925703243602E-01
H   -6.2244524884126584E-01   -1.9072903584365897E+00
2.9329726493504088E-01
H   -1.9547736115885346E+00   -9.0139495866835251E-01
-5.9918150655443085E-02
H   -6.1937432334401399E-01   -9.4837844365638890E-01
-1.2385015008153359E+00
H   -1.7075737360002088E-01    2.9731209011422616E-01
1.4541336191929111E+00
H    9.7457573875863202E-01    8.5636471630587491E-02
1.2656205437423565E-01
H   -5.0131648636893655E-01    1.6371906515892005E+00
-1.4111541759474644E+00
H   -1.5467719258289738E+00    1.7278640292584959E+00
-6.4073628967786178E-02
H    1.1121698319311175E+00    2.9201730368212155E+00
-7.3684782242081992E-01
H    1.8360961237017401E-02    3.5103940802614222E+00
4.9963333677363780E-01
H    1.1955573776036026E+00    2.3395752869018538E+00
9.7481281683867282E-01
    &END COORD
    &VELOCITY
    -9.1145154536295919E-05   -1.7288597297829858E-04
5.2498054992999613E-06
     1.6071166440413050E-06   -2.6329278272704861E-05
4.6405385077460174E-05
     2.8139550923834489E-04   -9.0163993819247976E-05
7.6949734768254173E-05
    -3.5140868375595375E-05    1.1591245497504604E-04
9.3441546132711488E-07
    -6.5449810886309572E-04    1.2949138600657238E-04
-9.6905572370049138E-05
    -5.5880056343657911E-04   -7.6023320034826296E-04
4.5331781519918144E-04
     7.8891547853511906E-05    3.9925263875885246E-04
-6.3042129441400981E-04
     3.8964847985305349E-05   -3.5437713203463964E-04
-1.1152482653525371E-03
     1.4947763296898738E-04   -3.9868429077368579E-04
1.7981274276414143E-04
     1.6902752937549336E-05    3.8798443523281535E-04
-1.6885685806997559E-04
    -1.0427106459532161E-03    1.3857405676144231E-04
2.8224441261646684E-04
     6.0553785519956553E-04    4.7716373383966196E-04
-5.7712612804223390E-04
    -7.8775588105202301E-04    1.2823159298612447E-03
7.1462951097974915E-05
     2.8652761625418420E-04    7.6557360110276226E-04
5.8106345621775769E-05
    &END VELOCITY
    &COLVAR
      &TORSION
        ATOMS 1 2 3 4
      &END TORSION
    &END
  &END SUBSYS
&END FORCE_EVAL
&MOTION
  &MD
    ENSEMBLE NVT
    STEPS 100000
    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 0.001
      TEMPERATURE 0.0
      NT_HILLS 100
      &METAVAR
        MASS 50.0
        LAMBDA 0.5
        COLVAR 1
        SCALE [rad] 0.5
      &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 16, 10:34 am, Teodoro Laino <teodor... at gmail.com> wrote:
> Would you mind show us your full input.
>
> Teo
>
> On 16 May 2008, at 08:33, ilya wrote:
>
>
>
> > Well, I mean that rotation begins independently of gaussian params
> > when the filled depth of the potential well is no more than 1 kcal/mol
> > (but should be about 7 for butane rotation).
> > I thought about what is called "hill surfing" but after more
> > experiments I don't think that it is the source of such behavior (I've
> > tried small hills and large stride).
>
> > Ilya.
>
> > On May 15, 8:47 pm, Axel <akoh... at gmail.com> wrote:
> >> On May 15, 10:13 am, ilya <ily... at gmail.com> wrote:
>
> >>> Hello!
>
> >>> Well, I performed another test reaction which is Cl- + CH3Cl  
> >>> (from the
> >>> article).
> >>> I have successfully build a 3d fes which is very similar to that one
> >>> in the article and I think I've got the idea of choosing parameters
> >>> for metadynamics.
> >>>    BUT
> >>> For the case of butane I can't obtain any adequate free energy
> >>> profile.
> >>> I observed that after some point  the molecule starts spinning
> >>> strangely around C2-C3 bond and I think the are still some bugs  
> >>> in the
>
> >> ilya,
>
> >> please describe "strangely".
> >> once you have filled all minima
> >> with gaussians you are supposed to
> >> have the molecule rotating freely
> >> around the C2-C3 bond (no more barrier
> >> left!).
>
> >> cheers,
> >>     axel.
>
> >>> case of periodic colvar in code.
> >>> Maybe someone else with more experience in metadynamics would  
> >>> also try
> >>> to do this? Maybe I am doing something wrong?