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.
|Project name||Targeted molecular dynamics (TMD) simulation|
|Samples requriements||The initial structure of PDB ID, etc.|
|Detection cycle||Depends on the time you need to simulate.|
|Service including||We provide you with raw data and calculation result analysis service.|
ComputaBio offers a corresponding targeted molecular dynamics (TMD) simulationOur team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. The ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific.