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Subsections


Accelerated Molecular Dynamics

Accelerated molecular dynamics (aMD) [29] is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. The method modifies the potential energy landscape by raising energy wells that are below a certain threshold level, while leaving those above this level unaffected. As a result, barriers separating adjacent energy basins are reduced, allowing the system to sample conformational space that cannot be easily accessed in a classical MD simulation.

Please include the following two references in your work using the NAMD implementation of aMD:

Theoretical background

In the original form of aMD [29], when the system's potential energy falls below a threshold energy, $ E$ , a boost potential is added, such that the modified potential, $ V^*({\bf r})$ , is related to the original potential, $ V({\bf r})$ , via

$\displaystyle V^*({\bf r})= V({\bf r}) + \Delta V({\bf r}),$ (62)

where $ \Delta V({\bf r})$ is the boost potential,

$\displaystyle \Delta V({\bf r})= \left \{ \begin{array}{l l} 0 & \quad \quad V(...
...r}))^2}{\alpha+E-V({\bf r})} & \quad \quad V({\bf r})<E. \\ \end{array} \right.$ (63)

As shown in the following figure, the threshold energy $ E$ controls the portion of the potential surface affected by the boost, while the acceleration factor $ \alpha $ determines the shape of the modified potential. Note that $ \alpha $ cannot be set to zero, otherwise the derivative of the modified potential is discontinuous.

Figure: Schematics of the aMD method. When the original potential (thick line) falls below a threshold energy $ E$ (dashed line), a boost potential is added. The modified energy profiles (thin lines) have smaller barriers separating adjacent energy basins.
Image amd_schematic
From an aMD simulation, the ensemble average, $ \langle A \rangle$ , of an observable, $ A({\bf r})$ , can be calculated using the following reweighting procedure:

$\displaystyle \langle A \rangle =\frac{\langle A({\bf r})\,\text{exp} (\beta \D...
...{\bf r})) \rangle^* } {\langle \text{exp} (\beta \Delta V({\bf r})) \rangle^*},$ (64)

in which $ \beta$ =$ 1/k_BT$ , and $ \langle ... \rangle$ and $ \langle...\rangle^*$ represent the ensemble average in the original and the aMD ensembles, respectively.

Currently, aMD can be applied in three modes in NAMD: aMDd, aMDT, and aMDdual [73]. The boost energy is applied to the dihedral potential in the aMDd mode (the default mode), and to the total potential in the aMDT mode. In the dual boost mode (aMDdual) [28], two independent boost energies are applied, one on the dihedral potential and the other on the (Total - Dihedral) potential.

NAMD parameters

The following parameters are used to enable accelerated MD:


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Next: Adaptive Tempering Up: Accelerated Sampling Methods Previous: Accelerated Sampling Methods   Contents   Index
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