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188
Bias
AT
the positions of the wall. The a_i in the expression for
a wall.
the force constant for the wall. The k_i in the
expression for a wall.
( default=0.0 ) the offset for the start of the wall. The
o_i in the expression for a wall.
( default=2.0 ) the powers for the walls. The e_i in the
expression for a wall.
( default=1.0 ) the values for s_i in the expression for a
wall
KAPPA
OFFSET
EXP
EPS
Options
NUMERICAL_DERIVATIVES
( default=off ) calculate the derivatives for these
quantities numerically
Examples
The following input tells plumed to add both a lower and an upper walls on the distance between atoms 3 and
5 and the distance between atoms 2 and 4. The lower and upper limits are defined at different values. The
strength of the walls is the same for the four cases. It also tells plumed to print the energy of the walls.
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias
(See also DISTANCE and PRINT).
7.5
METAD
This is part of the bias module
Used to performed MetaDynamics on one or more collective variables.
In a metadynamics simulations a history dependent bias composed of intermittently added Gaussian functions is
added to the potential [22].
d
(0)
(si − si (kτ))2
V (~s,t) = ∑ W (kτ) exp − ∑
2σi2
i=1
kτ<t
!
.
This potential forces the system away from the kinetic traps in the potential energy surface and out into the unexplored parts of the energy landscape. Information on the Gaussian functions from which this potential is composed
is output to a file called HILLS, which is used both the restart the calculation and to reconstruct the free energy as a
function of the CVs. The free energy can be reconstructed from a metadynamics calculation because the final bias
is given by:
V (~s) = −F(~(s))
During post processing the free energy can be calculated in this way using the sum_hills utility.
In the simplest possible implementation of a metadynamics calculation the expense of a metadynamics calculation
increases with the length of the simulation as one has to, at every step, evaluate the values of a larger and larger
number of Gaussians. To avoid this issue you can store the bias on a grid. This approach is similar to that proposed
in [23] but has the advantage that the grid spacing is independent on the Gaussian width. Notice that you should
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