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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
![$\displaystyle U_{TMD} = \frac{1}{2} \frac{k}{N} \left[ RMS(t) - RMS^*(t) \right]^2$](img146.png) |
(9) |
where
is the instantaneous best-fit RMS distance of the current
coordinates from the target coordinates, and
evolves linearly
from the initial RMSD at the first TMD step to the final RMSD at the last
TMD step. The spring constant
is scaled down by the number
of targeted
atoms.
- TMD
Is TMD active
Acceptable Values: on or off
Default Value: off
Description: Should TMD steering forces be applied to the system. If TMD is enabled,
TMDk, TMDFile, and TMDLastStep must be defined in the
input file as well.
- TMDk
Elastic constant for TMD forces
Acceptable Values: Positive value in
Å
.
Description: The value of
in Eq. 9. A value of 200 seems to work
well in many cases.
- TMDOutputFreq
How often to print TMD output
Acceptable Values: Positive integer
Default Value: 1
Description: TMD output consists of lines of the form TMD ts targetRMS currentRMS
where ts is the timestep, targetRMS is the target RMSD at that
timestep, and currentRMS is the actual RMSD.
- TMDFile
File for TMD information
Acceptable Values: Path to PDB file
Description:
Target atoms are those whose occupancy (O) is nonzero in the TMD PDB file.
The file must contain the same number of atoms as the structure file. The
coordinates for the target structure are also taken from the targeted
atoms in this file. Non-targeted atoms are ignored.
- TMDFirstStep
first TMD timestep
Acceptable Values: Positive integer
Default Value: 0
Description:
- TMDLastStep
last TMD timestep
Acceptable Values: Positive integer
Description: TMD forces are applied only between TMDFirstStep and TMDLastStep.
The target RMSD evolves linearly in time from the initial to the final target
value.
- TMDInitialRMSD
target RMSD at first TMD step
Acceptable Values: Non-negative value in Å
Default Value: from coordinates
Description:
In order to perform TMD calculations that involve restarting a previous
NAMD run, be sure to specify TMDInitialRMSD with the same value
in each NAMD input file, and use the NAMD parameter firstTimestep
in the continuation runs so that the target RMSD continues from where the
last run left off.
- TMDFinalRMSD
target RMSD at last TMD step
Acceptable Values: Non-negative value in Å
Default Value: 0
Description: If no TMDInitialRMSD is given, the initial RMSD will be calculated at the
first TMD step. TMDFinalRMSD may be less than or greater than
TMDInitialRMSD, depending on whether the system is to be steered
towards or away from a target structure, respectively. Forces are applied
only if
is betwween TMDInitialRMSD and
; in other
words, only if the current RMSD fails to keep pace with the target value.
Next: Steered Molecular Dynamics (SMD)
Up: User Defined Forces
Previous: Rotating Constraints
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