Applications of GROMACS Software

The GROMACS project started in 1991 and was developed by the Department of Biochemistry of the University of Groningen in the Netherlands (1991-2000). GROMACS is a versatile software package for performing molecular dynamics, that is, simulating Newton's equations of motion for systems with hundreds to millions of particles, and is a community-driven project. GROMACS is mainly used to simulate and study the properties of biomolecules such as proteins, lipids, and nucleic acids. Since GROMACS is very fast at calculating non-bonding interactions, many research groups also use it to study non-bonding interactions. Based on algorithm optimization, GROMACS is very efficient. Also, GROMACS is compiled and installed to expect optimal performance on a particular processor. It runs using a command line interface, uses file input and output, provides estimated time remaining (ETA) feedback, and provides a molecular trajectory viewer and molecular trajectory analysis extensions. In addition, GROMACS supports multiple force fields and can run in parallel, or use MPI for cluster computing.

Our Services Based on GROMACS Software Platform

GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis. Our scientists provide customers with simulation services on the GROMACS software platform to study the properties of biomolecules such as proteins, lipids, nucleic acids, etc.

• Umbrella Sampling
  Umbrella sampling is a technique used in computational physics and chemistry to improve systematic sampling. At CD ComputaBio, our scientists use umbrella sampling to overcome the pitfalls of systematic sampling. We help customers obtain coordinate files for structures of interest and generate topology from pdb2gmx. Some systems require special consideration.
• Free Energy of Solvation
  At CD ComputaBio, our scientists applied GROMACS to free energy calculations, including free energies of solvation/hydration and free energies of small molecules bound to some larger acceptor biomolecules (usually proteins).
• Replica Exchange Molecular Dynamics (REMD)
  Because complex biomolecules have many local minimum energy states, traditional MD simulations often get stuck in one of the local minima, resulting in unreliable free energy distributions. Using the GROMACS program, we can perform several types of REMD.
• Steered Molecular Dynamics (SMD)
  Steering molecular dynamics (SMD) induces the unbinding of ligands and the conformational changes of biomolecules on a timescale that can be used for molecular dynamics simulations. CD ComputaBio provides two SMD simulations:
  • Constant force simulations
  • Constant speed simulations
• Building Biphasic Systems
  At CD ComputaBio, our scientists can build heterogeneous biphasic systems and lipid bilayer systems consisting of hydrophobic and hydrophilic layers for customers on the GROMACS software platform.
• Building Protein-Ligand Complex
• Preparing the protein topology
• Preparing the ligand topology
• Defining the unit cell & adding solvent
• Energy minimization
• Equilibration
• Production MD

Features of GROMACS Software

• GROMACS supports basic dynamics related algorithms, including Newtonian mechanics and stochastic dynamics integrators, energy minimization, canonical mode analysis, simulated quenching, and more.
• GROMACS has built-in support for many common classical force fields such as AMBER, CHARMM, GROMOS and OPLS, as well as several less common force fields.
• GROMACS supports Martini coarse-grained models.
• GROMACS supports GBSA-based implicit solvent models, including three optional methods for calculating Born radii.
• GROMACS supports QM/MM hybrid dynamics, and the calculation methods supported in the QM part include AM1, PM3, RHF, UHF, DFT, B3LYP, MP2, CASSCF and MMVB.

Project Sample

Our computational biology team has extensive experience in the research of REMD on our GROMACS 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.

Related Links

GROMACS Tutorial