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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 TMDFile. Forces on the atoms will be calculated for each domain independently of the other domains.

Within each domain, the set of atoms used to fit the target structure can be different from the set of atoms that are biased towards the target structure. If the altloc field in the TMDFile is not ` ' or `0' then the atom is fitted. If the occupancy is non-zero then the atom is biased. If none of the atoms in a domain have altloc set then all biased atoms are fitted.

Note that using different atoms for fitting and biasing or not using the same spring constant for all target atoms within a domain will result in forces conserving neither energy nor momentum. In this case harmonic restraints and Langevin dynamics are likely needed.


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