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Targeted Molecular Dynamics (TMD)

In TMD, subset of atoms in the simulation is guided towards a final 'target' structure by means of steering forces. At each timestep, the RMS distance between the current coordinates and the target structure is computed (after first aligning the target structure to the current coordinates). The force on each atom is given by the gradient of the potential

$\displaystyle U_{TMD} = \frac{1}{2} \frac{k}{N} \left[ RMS(t) - RMS^*(t) \right]^2$ (31)

where $ RMS(t)$ is the instantaneous best-fit RMS distance of the current coordinates from the target coordinates, and $ RMS^*(t)$ evolves linearly from the initial RMSD at the first TMD step to the final RMSD at the last TMD step. The spring constant $ k$ is scaled down by the number $ N$ of targeted atoms. Atoms can be separated into non-overlapping constraint domains by assigning integer values in the beta column of the .pdb file. Forces on the atoms will be calculated for each domain independently of the other domains.


next up previous contents index
Next: Steered Molecular Dynamics (SMD) Up: User Defined Forces Previous: Symmetry Restraints   Contents   Index
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