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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