All-Atom Molecular Dynamics (MD) Simulations

All-atom molecular dynamics (MD) simulations have revolutionized the field of computational chemistry and biochemistry. By simulating the dynamic behavior of atoms and molecules, MD simulations provide valuable insights into the behavior and interactions of complex systems at the atomic level. This method performs simulations according to Newton's laws of motion, where each atom is treated as an individual particle in the mathematical model.

Our Services

All-Atom MD Simulation Systems

Figure 1. All-atom molecular dynamics.

  • Protein-ligand Interactions
  • Protein Folding and Stability
  • Enzyme Catalysis Mechanism Studies
  • Membrane Protein Dynamics
  • Drug Delivery Systems
  • Material Properties
  • Protein-protein Interactions
  • Protein-protein Interactions
  • Nucleic Acid Dynamics

All-Atom MD Simulation Analysis

Figure 2. CoVID-19 research using molecular molecular dynamics.

  • Backbone Fluctuations: RMSD, RMSF.
  • Interactions: hydrogen bonding, salt bridges, angles, dihedral angles, hydration, interaction spectra.
  • Binding free energy: MM/PB(GB)SA.
  • Conformational Sampling: clustering, PCA, simple normal mode analysis, secondary structure analysis, potential energy surface scanning, dominant conformation identification.

Force Fields for All-Atom Molecular Dynamics Simulations

CHARMM Force Fields

CHARMM force fields can handle a variety of macromolecules, including organic molecules, polymers, biochemical molecules, and so on. The structures, conformational energies and free energies obtained by such force fields often match experimental values.

AMBER Force Fields

The situation of the potential energy function of the AMBER force field is relatively simple, requiring few parameters and a relatively small amount of computation. AMBER force field is mainly used to study biological molecules such as proteins, nucleic acids, and polysaccharides.

OPLS-AA Force Fields

The OPLS-AA force field has been developed for calculations on organic liquids, dilute aqueous solutions, hydrogen bonding, and ionic water complexes, and provides a set of functions describing the non-bonding interactions of proteins in crystals or aqueous solutions.

Overall Solutions

At CD ComputaBio, we offer a comprehensive range of All-atom molecular dynamics simulation services tailored to meet your specific research goals. As a leading computational chemistry company, we possess extensive expertise in simulating and analyzing the dynamic behavior of molecular systems at the atomic level. Our team of experienced scientists and researchers are dedicated to providing high-quality services to clients from diverse scientific areas, including drug discovery, material science, and biochemistry.

Figure 3. RMSD calculation results of all-atom molecular dynamics.

1. System Preparation

We specialize in preparing molecular systems for MD simulations to ensure the accuracy and reliability of the simulation process.

2. Equilibration

Our team performs equilibrium runs on your system, carefully monitoring the relevant thermodynamic parameters.

3. Production Simulation

We perform extensive production simulations to generate comprehensive and meaningful data about your system.

Workflow of Our Service

Figure 4. Workflow of our all-atom molecular dynamics service.

Our Advantages

Atomic-level Detail: MD simulations provide a detailed description of molecular behavior, allowing researchers to study complex systems at the atomic level. This level of detail is invaluable in understanding molecular mechanisms, conformational changes, and molecular interactions.

Predictive Capabilities: By accurately capturing the dynamic behavior of molecules, MD simulations can provide predictions of system behavior, aiding in the design and optimization of drugs, materials, and biological systems.


  1. Padhi A K, Rath S L, Tripathi T. Accelerating COVID-19 research using molecular dynamics simulation. The Journal of Physical Chemistry B, 2021, 125(32): 9078-9091.
  2. Patil O, Manikandan D, Nandigana V V R. A molecular dynamics simulation framework for predicting noise in solid-state nanopores. Molecular Simulation, 2020, 46(13): 1011-1016.
  3. Marcello DeLuca. et al. Prediction and Control in DNA Nanotechnology. ACS Applied Bio Materials, 2023.
* For Research Use Only.