Targeted Molecular Dynamics (TMD) Simulation

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:

Targeted molecular dynamics (TMD) simulation 1

Where RMS is the instantaneous best-fit RMS distance of the current coordinates from the target coordinates, and RMS evolves linearly from the initial RMSD at the first TMD step to the final RMSD at the last TMD step. 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.


  • In TMD, the force field is supplemented with harmonic constraints that promote an increase in the conformational distance from the original state or a decrease in the distance from the target unfolded structure.
  • As a basis for comparison, the unfolding process can be simulated by conventional (ie unconstrained) molecular dynamics at 375 and 475 K.
  • In all simulations, the solvated implicit approximate adiabatic is used to simulate the solvent response, which is suitable for the simulation method used here for nanosecond expansion. The CI2 simulation performed by the dosing model showed a similar sequence of events.

Our simulation services

Project name Targeted molecular dynamics (TMD) simulation
Samples requirement The initial structure of PDB ID, etc.
Timeline Depends on the time you need to simulate.
Deliverables We provide you with raw data and calculation result analysis service.
Price Inquiry

Targeted molecular dynamics (TMD) simulation 2

Our advantages

  • Molecular dynamics simulation saves a lot of labor costs.
  • Short calculation period and fast speed.
  • The funds required are far less than biological or chemical experiments.
  • High calculation accuracy.

Our molecular dynamics simulation services

CD ComputaBio provides corresponding targeted molecular dynamics (TMD) simulations. Our expert team can provide up to one millisecond of simulation time for the system of your choice, so you don't have to worry about technical issues. We can also provide you with relevant results analysis services.

* For Research Use Only.