Applications of GROMOS Software

Groningen Molecular Simulation (GROMOS) is the name of the force field used for molecular dynamics simulations, and associated computer software packages. Both were developed in the computer-aided Chemistry group at the University of Groningen and the Laboratory of Physical Chemistry at the Swiss Federal Institute of Technology (ETH Zurich). In Groningen, Herman Berendsen was involved in its development. GROMOS96 has been developed for dynamic modeling of (bio)molecules using molecular dynamics, stochastic dynamics and energy minimization methods as well as path integral forms.

Our Services Based on GROMOS Software

GROMOS can achieve better accuracy than existing widely used or state-of-the-art methods in predicting the structure of ligand-protein complexes. On the GROMOS software platform, CD ComputaBio can provide the listed services:

• Molecular Dynamics Sampling Simulation
  CD ComputaBio utilizes advanced MD simulation techniques to facilitate the study of conformational dynamics of proteins and protein ligands, and we can combine MD simulations with molecular docking methods for in silico virtual screening.
• Analysis of the MD trajectories
• Identifying allosteric binding sites provides strategies for modulating target activity through allosteric ligands.
• Identify hidden binding sites and characterize their draggability.
• Study the kinetics and thermodynamics of ligand binding to target proteins.
• Analysis of the Energy Trajectory
  GROMOS can write energies, free energy λ derivatives, and their block averages to separate trajectory files for later analysis.
• Analysis of the Coordinate Trajectory
  Our scientists use the program frameout to generate PDB snapshots from simulated trajectory (or any other) coordinate files.
• Free Energy Calculations
  We will now use this program to calculate the solvation free energy of ions, proteins, and small molecules in water.
• Enveloping Distribution Sampling
  There are many large potential energy barriers that prevent proteins from transitioning from one minimum-energy conformation to another. Our scientists use GROMOS' Local Elevation to increase sampling

Our Capabilities

• We use MD simulation methods to provide detailed information on protein and nucleic acid fluctuations and conformational changes, and to study your macromolecular systems of interest.
• We can map ligand binding sites and analyze binding modes, providing compelling strategies for modulating target activity through these ligands.
• We support the discovery of cryptic binding sites and their characterization of their draggability.
• Our experts help you gain insight into complex affinities and quantify energy changes throughout the process.

Features of GROMOS Software

• The code is transparent and easy to modify
• Modular architecture, new functions designed by users only need to be modified in part;
• Independence of simulation code and force field
• The independence of simulation code and computer hardware.
• Calculates free energy changes based on coupled parameter methods using thermodynamic integration, slow growth, or one-step perturbation, possibly including soft-core non-bonded interactions.
• Spatial boundary conditions are defined by the shape, size, and orientation of the simulated system, as well as the properties of the boundary and its surroundings.

Project Sample

Our computational biology team has extensive experience in the research of MD on our GROMOS software platform. The following is a small snapshot of our research process for reference only. For details, please feel free to consult our professional team.