GROMOS energy functions

Molecular modeling and computer simulation with empirical potential energy function (force field) are now routinely carried out to help understand and predict structures and dynamics of proteins and other macromolecules of biological relevance in water and membrane environments. After over 40 years of development, popular force fields such as AMBER, CHARMM, OPLS and GROMOS have been widely employed in biomolecular simulations. These force fields are used dominantly in highly optimized molecular dynamics... 

CHARMM The Energy Function and Its Parameterization Force Fields A Brief Introduction Force Fields A General Discussion Force Fields MM3 Force Fields MMFF94 GROMOS Force Field. 

The simulation methodologies applied to proteins and nucleic acids are applicable to the biomembrane modeling at the atomic level. The jvidely distributed programs, CHARMM, AMBER, and GROMOS, have been applied for biomembrane studies. The common energy parameters of proteins, nucleic acids, and water are used with minor modifications for lipids. For instance, the AMBER energy function is written as follows ... 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

Biological and Organic Molecules Anharmonic Molecular Force Fields Carbocation Force Fields Carbohydrate Force Fields CHARMM The Energy Function and Its Parameterization Force Fields A Brief Introduction Force Fields A General Discussion Force Fields CFF Force Fields MM3 GROMOS Force Field and OPLS Force Fields). The multitudinous issues related to achieving convergence will be discussed below. 

AMBER A Program for Simulation of Biological and Organic Molecules Biomembranes Modeling CHARMM The Energy Function and Its Parameterization Environment of a Membrane Protein Force Fields A General Discussion GROMOS Force Field Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Permeation of Lipid Membranes Molecular Dynamics Simulations Time Correlation Functions. 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

Fig. 8.3 Free energy profiles along the S-S -C-C dihedral angle of the disulfide bridge of the 127 protein as a function of external force. The profile has been obtained from force-field molecular dynamics simulations carried out with GROMOS at r = 300 K. The model system in these simulations comprises the 127 protein and SPC water molecules solvating the protein in a tetragonal box. The relevant S-S-C-C conformers of the disulfide bridge embedded in the protein are shown on top using a partial and schematic representation. Courtesy of Padmesh Anjukandi...

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