next up previous contents index
Next: Metadynamics Up: Biasing and analysis methods Previous: Biasing and analysis methods   Contents   Index


Adaptive Biasing Force

For a full description of the Adaptive Biasing Force method, see reference [38]. For details about this implementation, see references [39] and [40]. When publishing research that makes use of this functionality, please cite references [38] and [40].

An alternate usage of this feature is the application of custom tabulated biasing potentials to one or more colvars. See inputPrefix and updateBias below.

ABF is based on the thermodynamic integration (TI) scheme for computing free energy profiles. The free energy as a function of a set of collective variables $ {\mbox{\boldmath {$\xi$}}}=(\xi_{i})_{i\in[1,n]}$ is defined from the canonical distribution of $ {\mbox{\boldmath {$\xi$}}}$ , $ {\mathcal P}({\mbox{\boldmath {$\xi$}}})$ :

$\displaystyle A({\mbox{\boldmath {$\xi$}}}) = -\frac{1}{\beta} \ln {\mathcal P}({\mbox{\boldmath {$\xi$}}}) + A_0$ (13.14)

In the TI formalism, the free energy is obtained from its gradient, which is generally calculated in the form of the average of a force $ {\mbox{\boldmath {$F$}}}_\xi$ exerted on $ {\mbox{\boldmath {$\xi$}}}$ , taken over an iso- $ {\mbox{\boldmath {$\xi$}}}$ surface:

$\displaystyle {\mbox{\boldmath {$\nabla$}}}_\xi A({\mbox{\boldmath {$\xi$}}}) =...
...t\langle -{\mbox{\boldmath {$F$}}}_\xi \right\rangle_{\mbox{\boldmath {$\xi$}}}$ (13.15)

Several formulae that take the form of (13.16) have been proposed. This implementation relies partly on the classic formulation [41], and partly on a more versatile scheme originating in a work by Ruiz-Montero et al. [42], generalized by den Otter [43] and extended to multiple variables by Ciccotti et al. [44]. Consider a system subject to constraints of the form $ \sigma_{k}({\mbox{\boldmath {$x$}}}) = 0$ . Let ( $ {\mbox{\boldmath {$v$}}}_{i})_{i\in[1,n]}$ be arbitrarily chosen vector fields ( $ \mathbb{R}^{3N}\rightarrow\mathbb{R}^{3N}$ ) verifying, for all $ i$ , $ j$ , and $ k$ :

$\displaystyle {\mbox{\boldmath {$v$}}}_{i} \cdot \mbox{\boldmath$\nabla_{\!\!x}\,$}\xi_{j}$ $\displaystyle =$ $\displaystyle \delta_{ij}$ (13.16)
$\displaystyle {\mbox{\boldmath {$v$}}}_{i} \cdot \mbox{\boldmath$\nabla_{\!\!x}\,$}\sigma_{k}$ $\displaystyle =$ 0 (13.17)

then the following holds [44]:

$\displaystyle \frac{\partial A}{\partial \xi_{i}} = \left\langle {\mbox{\boldma...
...\,$}\cdot {\mbox{\boldmath {$v$}}}_{i} \right\rangle_{\mbox{\boldmath {$\xi$}}}$ (13.18)

where $ V$ is the potential energy function. $ {\mbox{\boldmath {$v$}}}_{i}$ can be interpreted as the direction along which the force acting on variable $ \xi_{i}$ is measured, whereas the second term in the average corresponds to the geometric entropy contribution that appears as a Jacobian correction in the classic formalism [41]. Condition (13.17) states that the direction along which the system force on $ \xi_{i}$ is measured is orthogonal to the gradient of $ \xi_{j}$ , which means that the force measured on $ \xi_{i}$ does not act on $ \xi_{j}$ .

Equation (13.18) implies that constraint forces are orthogonal to the directions along which the free energy gradient is measured, so that the measurement is effectively performed on unconstrained degrees of freedom.

In the framework of ABF, $ {\bf F}_\xi$ is accumulated in bins of finite size $ \delta \xi$ , thereby providing an estimate of the free energy gradient according to equation (13.16). The biasing force applied along the collective variables to overcome free energy barriers is calculated as:

$\displaystyle {\bf F}^{\rm ABF} = \alpha(N_\xi) \times$   $\displaystyle \mbox{\boldmath$\nabla_{\!\!x}\,$}$$\displaystyle \widetilde A({\mbox{\boldmath {$\xi$}}})$ (13.19)

where $ \nabla_{\!\!x}\,$ $ \widetilde A$ denotes the current estimate of the free energy gradient at the current point $ {\mbox{\boldmath {$\xi$}}}$ in the collective variable subspace, and $ \alpha(N_\xi)$ is a scaling factor that is ramped from 0 to 1 as the local number of samples $ N_\xi$ increases to prevent nonequilibrium effects in the early phase of the simulation, when the gradient estimate has a large variance. See the fullSamples parameter below for details.

As sampling of the phase space proceeds, the estimate $ \nabla_{\!\!x}\,$ $ \widetilde A$ is progressively refined. The biasing force introduced in the equations of motion guarantees that in the bin centered around $ {\mbox{\boldmath {$\xi$}}}$ , the forces acting along the selected collective variables average to zero over time. Eventually, as the undelying free energy surface is canceled by the adaptive bias, evolution of the system along $ {\mbox{\boldmath {$\xi$}}}$ is governed mainly by diffusion. Although this implementation of ABF can in principle be used in arbitrary dimension, a higher-dimension collective variable space is likely to result in sampling difficulties. Most commonly, the number of variables is one or two.

ABF requirements on collective variables

  1. Only linear combinations of colvar components can be used in ABF calculations.
  2. Availability of system forces is necessary. The following colvar components can be used in ABF calculations: distance, distance_xy, distance_z, angle, dihedral, gyration, rmsd and eigenvector. Atom groups may not be replaced by dummy atoms, unless they are excluded from the force measurement by specifying oneSiteSystemForce, if available.
  3. Mutual orthogonality of colvars. In a multidimensional ABF calculation, equation (13.17) must be satisfied for any two colvars $ \xi_{i}$ and $ \xi_{j}$ . Various cases fulfill this orthogonality condition:
  4. Mutual orthogonality of components: when several components are combined into a colvar, it is assumed that their vectors $ {\mbox{\boldmath {$v$}}}_{i}$ (equation (13.19)) are mutually orthogonal. The cases described for colvars in the previous paragraph apply.
  5. Orthogonality of colvars and constraints: equation 13.18 can be satisfied in two simple ways, if either no constrained atoms are involved in the force measurement (see point 3 above) or pairs of atoms joined by a constrained bond are part of an atom group which only intervenes through its center (center of mass or geometric center) in the force measurement. In the latter case, the contributions of the two atoms to the left-hand side of equation 13.18 cancel out. For example, all atoms of a rigid TIP3P water molecule can safely be included in an atom group used in a distance component.

Parameters for ABF

ABF depends on parameters from collective variables to define the grid on which free energy gradients are computed. In the direction of each colvar, the grid ranges from lowerBoundary to upperBoundary, and the bin width (grid spacing) is set by the width parameter (see 13.2.1). The following specific parameters can be set in the ABF configuration block (in addition to generic bias parameters such as colvars - section 13.5):

Output files

The ABF bias produces the following files, all in multicolumn ASCII format:

If several ABF biases are defined concurrently, their name is inserted to produce unique filenames for output, as in outputName.abf1.grad. This should not be done routinely and could lead to meaningless results: only do it if you know what you are doing!

Post-processing: reconstructing a multidimensional free energy surface

If a one-dimensional calculation is performed, the estimated free energy gradient is automatically integrated and a potential of mean force is written under the file name <outputName>.pmf, in a plain text format that can be read by most data plotting and analysis programs (e.g. gnuplot).

In dimension 2 or greater, integrating the discretized gradient becomes non-trivial. The standalone utility abf_integrate is provided to perform that task. abf_integrate reads the gradient data and uses it to perform a Monte-Carlo (M-C) simulation in discretized collective variable space (specifically, on the same grid used by ABF to discretize the free energy gradient). By default, a history-dependent bias (similar in spirit to metadynamics) is used: at each M-C step, the bias at the current position is incremented by a preset amount (the hill height). Upon convergence, this bias counteracts optimally the underlying gradient; it is negated to obtain the estimate of the free energy surface.

abf_integrate is invoked using the command-line:

integrate <gradient_file> [-n <nsteps>] [-t <temp>] [-m (0|1)]
                          [-h <hill_height>] [-f <factor>]

The gradient file name is provided first, followed by other parameters in any order. They are described below, with their default value in square brackets:

Using the default values of all parameters should give reasonable results in most cases.

abf_integrate produces the following output files:

Note: Typically, the ``deviation'' vector field does not vanish as the integration converges. This happens because the numerical estimate of the gradient does not exactly derive from a potential, due to numerical approximations used to obtain it (finite sampling and discretization on a grid).

next up previous contents index
Next: Metadynamics Up: Biasing and analysis methods Previous: Biasing and analysis methods   Contents   Index