Steered Molecular Dynamics (SMD) Service

Steered molecular dynamics (SMD) service

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.

Our simulation services

Project name Steered molecular dynamics (SMD).
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.
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Our Steered molecular dynamics (SMD) 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.

Steered molecular dynamics (SMD) service 1

Features

  • Manipulating molecular dynamics.
  • Interactive molecular dynamics.
  • Visualization program for displaying, animating and analyzing biomolecular systems.

We provide a variety of molecular dynamics simulation service, but not limited to:

Our advantage

  • Assistance and support at every step throughout the application process.
  • Our team has been working in this field for more than ten years.
  • We can provide you with customized simulation services.
  • Short simulation period.
  • No hidden costs.

Steered molecular dynamics (SMD) service 2

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.

* It should be noted that our service is only used for research, not for clinical use.

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