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:
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.
|Targeted molecular dynamics (TMD) simulation
|The initial structure of PDB ID, etc.
|Depends on the time you need to simulate.
|We provide you with raw data and calculation result analysis service.
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.