Numerous experimental methodologies exist for directly probing the mechanical responses of a single biopolymer. Key methods are atomic force microscopy (AFM) in force spectroscopy mode, laser optical tweezers, magnetic tweezers, and the centrifuge force microscope. However, all these methods reveal only very limited microscopic detail on the molecular basis of the corresponding mechanical response. Steered molecular dynamics (SMD) simulations apply, in addition to intrinsic forces, external forces to biomolecules. These simulations mimic the experimental methodologies described above and, in addition, provide a unique atom-by-atom dynamical view of the protein's mechanical response. The standard SMD methodology and two variations (implemented through the NAMD/Tcl interface) will be briefly described below.
|Project name||Steered molecular dynamics (SMD).|
|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.|
CD ComputaBio provides two SMD simulations: constant force simulations and constant speed simulations:
Constant force simulations
|In the constant force SMD simulation, the force is directly applied to one or more atoms, and its extension or displacement is monitored throughout the dynamic process.|
Constant speed simulations
|In constant-speed SMD simulation, the harmonic potential of the motion (spring) is used to induce motion along the reaction coordinates. The free end of the spring (represented by virtual atoms) moves at a constant speed, while the protein atoms attached to the other end of the spring are subjected to the steering force.|
MD simulations have usually been limited to nanoseconds, with SMD simulations using non-physiological stretching speeds to induce conformational changes within this achievable time scale. CD ComputaBio can provide SMD simulations technology. Our team has worked in this field for more than ten years and published findings in top scientific journals.