Groningen molecular simulation (GROMOS) is one of the force fields commonly used in biomolecular simulations today, derived from the software package GROMOS for biomolecular simulations, in which a series of force fields were developed for application in this software. From the original GRO-MOS87, and GROMOS96 to the current widely used GROMOS45A3. These GROMOS force fields are integrated atomic force fields, and the force field parameters of these fields are mainly derived by fitting experimental data using the thermodynamic characteristics of pure or mixed fluid systems in the condensed state. Alfa Chemistry can provide customers with MD simulation services through the GROMOS force field.
Fig 1. The GROMOS 54A7 force field also successfully sampled the halogen bonded conformations in the molecular dynamic simulation of bacteriophage T4 lysozyme coupled with the iodobenzene or iodopentafluorobenzene molecules. (Zhu Z, et al. 2020)
For GROMOS-like force fields, the functional form of a typical force field is described below. RF represents the contribution of the reaction field to electrostatic interactions.
Fig 2. Functional form of a typical force field in GFROMOS. (Petrov D, et al. 2013)
Customers prefer GROMOS force fields due to their widespread use, great reproducibility of experimental results, and generic parameter transferability of the same chemical groups in various compounds. Van der Waals interactions, electrostatic interactions, and other non-bonding interaction parameters are calculated using the force field.
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The GROMOS force field is suitable for the simulation of alkanes, proteins, and nucleic acid condensed phases with a simple functional form. It is available in the following versions.
- G43B1: Suitable for simulations under vacuum.
- G43A1: The earliest GROMOS96 force field, which is a joint atomic force field, is used for condensed phases.
- G43A2: Improved dihedral angle parameter for atomic types in alkanes.
- G45A3: VDW parameters of alkanes were changed to better match experimental data (enthalpy of gasification, compressibility, pressure, the heat of hydration, etc.)
- G45A4: Added dihedral angle parameters, and atom types, and changed atomic charges to improve the simulation of nucleic acids.
- G53A5 and G53A6: Parameters were adjusted to make the free enthalpies of solubility of biomolecules (proteins, DNA, sugars, lipids) in cyclohexane and water close to the experimental values, respectively.
- G54A7/B7: The psi/phi torsion angle parameter was modified to correct the stability problem for helices when simulating proteins, an atomic type of -CH3 was added, Na+ and Cl- were modified to match their hydration energies, and an IMPROPER term related to the chiral change was added. The stability of the simulated protein is better than that of G53A6.
Alfa Chemistry provides global customers with fast, professional, high-quality MD simulation services at competitive prices, which can reduce the cost of late-stage experiments. We need to evaluate each project before we can determine the corresponding analysis plan and price. If you are interested in our services, please contact us for more details.
- Zhu Z, et al. (2020). "Interaction Nature and Computational Methods for Halogen Bonding: A Perspective." J. Chem. Inf. Model. 60(6): 2683-2696.
- Petrov D, et al. (2013). "A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications." PLoS Comput Biol. 9(7): e1003154.