PMF for butane rotation

ilya ily... at gmail.com
Wed Apr 23 12:48:59 UTC 2008


Hi !!!

I'm trying to perform a test metadynamics run to obtain free energy
profile for butane C2-C3 torsion rotation.
I've prepared an input according to examples, but when I execute the
simulation the molecule blows up after a hundred of steps.
Here is the input

&FORCE_EVAL
  METHOD QS
  &DFT
    &QS
      METHOD AM1
      &SE
        ANALYTICAL_GRADIENTS T
      &END
    &END QS
    &SCF
      SCF_GUESS ATOMIC
    &END SCF
  &END DFT
  &SUBSYS
    &CELL
      ABC 20.0 20.0 20.0
      UNIT ANGSTROM
      PERIODIC NONE
    &END CELL
    &COORD
      C            1.59125586     0.41342479     0.14003727
      C            0.32252829     1.16124839     0.52263341
      C           -0.84910157     0.43265546    -0.11376540
      C           -1.94048663     1.46412511    -0.50840178
      H            1.52870579    -0.60735277     0.37898357
      H            1.74514439     0.42933751    -0.91517059
      H            2.40297038     0.84409489     0.68368432
      H            0.30718345     1.26800062     1.63077856
      H            0.42763214     2.20188061    -0.01524355
      H           -0.68227576    -0.15483956    -1.02552216
      H           -1.22868583    -0.36692588     0.50963056
      H           -2.35282430     1.89592861     0.40350185
      H           -1.56059968     2.32543646    -1.17180146
      H           -2.80524537     1.06601703    -0.96111067
    &END COORD
    &COLVAR
      &TORSION
        ATOMS 1 2 3 4
      &END TORSION
    &END
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT_NAME BUTANE
  RUN_TYPE MD
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVT
    STEPS 5000
    TIMESTEP 0.5
    TEMPERATURE 300.0
    &THERMOSTAT
      &NOSE
      &END NOSE
    &END THERMOSTAT
  &END MD
  &PRINT
    &VELOCITIES OFF
    &END
    &TRAJECTORY
    &END
  &END
  &FREE_ENERGY
    &METADYN
      DO_HILLS
      LAGRANGE
      WW 0.001
      &METAVAR
        LAMBDA 1.0
        MASS 10.0
        SCALE 0.1
        COLVAR 1
      &END METAVAR
      &PRINT
        &COLVAR
          &EACH
            METADYNAMICS 100
          &END
        &END COLVAR
        &HILLS
          &EACH
            METADYNAMICS 100
          &END
        &END HILLS
      &END
    &END METADYN
  &END FREE_ENERGY
&END MOTION

Is it possible to obtain a detailed description of input somewhere
(more then in input manual) or could someone make needed corrections
in my input or to explain what am I doing incorrect (should I
experiment with metadynamics parameters, add walls or something
else?). It would be great.

Thanks a lot.
Best regards,
Ilya.


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