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DNA/RNA Molecular Dynamics Simulation


Nucleic acids play a key role in almost all aspects of life and are major functional players in biology. Nucleic acid derivatives and analogues are used to address targeted therapies for various diseases, biosensor technologies, molecular biology, and biotechnology. Molecular simulations have become an important tool for biochemical research. When they work properly, they can provide valuable interpretation of experimental results and ultimately provide novel, experimentally testable predictions.

In the study of nucleic acids (DNA/RNA), molecular dynamics (MD) simulation is a crucial technique. MD provides detailed structural and kinetic insights, which explains its recent transformation from a handful of highly specialized laboratories to a large group dealing with challenging biological problems. Alfa Chemistry provides top-notch DNA/RNA MD simulation services to its customers.

DNA/RNA Molecular Dynamics Simulation

Our Services

Alfa Chemistry uses cutting-edge digital techniques to study the molecular dynamics of DNA/RNA systems. mD modeling is performed using the AMBER 14 software package and parallel computing on CPUs and GPUs with CUDA architecture. ff99bsc0 and ff99bsc0+chiOL3 force fields are used for DNA and RNA, respectively. The ff99bsc0 and ff99bsc0+chiOL3 force fields were used for DNA and RNA, respectively. Electrostatic interactions were calculated by the particle grid Ewald method. The system pressure is 1 bar; the temperature in the system is maintained by scaling the velocity of the atoms with a period of 10 ps. The simulation step was increased to 2 fs using the SHAKE algorithm, and the coordinates of each atom in the system were recorded every 10 ps of the simulation. Double-stranded bodies and single-stranded oligonucleotides are placed in a cubic cell. The amount of water in the simulated cell was in the range of 4000-8000 molecules. Sodium ions are used to neutralize the negative charge accounted for in the periodic cell.

Project NameDNA/RNA Molecular Dynamics Simulation Service
DeliverablesWe provide all raw data and analysis services to our customers.
Samples RequirementThe initial structure of the DNA or RNA, PDB ID, etc.
Timeline DecideAccording to customers' needs
PricePlease contact us for an inquiry

The simulation process includes the following steps:

  • Creation of a PDB file that contains data on the coordinates of each atom in the structure of a duplex or single-stranded nucleic acid.
  • Creation of a water environment; addition of sodium ions to neutralize the periodic system.
  • Minimization of the entire system with a fixed nucleic acid.
  • Heating of the system with a fixed nucleic acid.
  • Equilibrating the density of the system.
  • Equilibrating the system at a constant pressure and a temperature.
  • MD simulation in an NPT ensemble.

Examples of nucleic acid interactions in biological systems.Fig 1. Examples of nucleic acid interactions in biological systems. (Yoo J, et al. 2020)

Our Advantages

  • The researchers all come from renowned universities or research centers and have extensive backgrounds in the simulation of protein molecular dynamics.
  • On a wide range of linked themes, we have either worked on our own or offered support to our clients. Numerous findings from the calculations and tests have been published in a number of major SCI publications in the field of life sciences.

Alfa Chemistry is committed to providing customers with high-end and high-quality technical services, and has rich practical experience and core technologies in DNA and RNA MD simulation. The service will provide accurate simulations of DNA and RNA structure and behavior, which have proven to be very helpful in a variety of related biological studies. Please contact us.


  • Yoo J, et al. (2020). "Molecular Dynamics Simulations of DNA-DNA and DNA-Protein Interactions." Current Opinion in Structural Biology. 64: 88-96.

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