Force fields biomolecular

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

Significant progress in the optimization of VDW parameters was associated with the development of the OPLS force field [53]. In those efforts the approach of using Monte Carlo calculations on pure solvents to compute heats of vaporization and molecular volumes and then using that information to refine the VDW parameters was first developed and applied. Subsequently, developers of other force fields have used this same approach for optimization of biomolecular force fields [20,21]. Van der Waals parameters may also be optimized based on calculated heats of sublimation of crystals [68], as has been done for the optimization of some of the VDW parameters in the nucleic acid bases [18]. Alternative approaches to optimizing VDW parameters have been based primarily on the use of QM data. Quantum mechanical data contains detailed information on the electron distribution around a molecule, which, in principle, should be useful for the optimization of VDW... 

Oostenbrink, C., Villa, A., Mark, A. E., Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation the GROM OS force-field parameter sets 53A5 and 53A5. J. Comput. Chem. 2004, 25, 1555-1575. 

As a first comparison between the QM/MM description of the dipeptide and its analogs in terms of standard biomolecular force fields we compared the quantum electrostatic field with the equivalent quantities resulting from purely classical MD runs with the AMBER95 [86] and the GROMOS96 [85] force fields. 

The Lennard-Jones potential continues to be used in many force fields, particularly those targeted for use in large systems, e.g., biomolecular force fields. In more general force fields targeted at molecules of small to medium size, slightly more complicated functional forms, arguably having more physical justification, tend to be used (computational times for small molecules are so short dial the efficiency of the Lennard-Jones potential is of little consequence). Such forms include the Morse potential [Eq. (2.5)] and the Hill potential... 

Transferability, using the same set of parameters to model a series of related molecules, is an important feature of a force field. Concerning the specialized biomolecular force fields, their transferability varies. For example, AMBER is more transferable than CHARMM especially with recent efforts on more automated methods of parameter assignment. 129,193 Essentially the quality of a force field depends on how appropriate is the mathematical form of the energy expression and how accurate are the parameters. 

Hess, B., van der Vegt, N.F.A. Hydration thermodynamic properties of amino acid analogues A comparison of biomolecular force fields and water models, J. Phys. Chem. B 2006,110,17616-26. 

In a series of papers, Stock and coworkers have combined the quasiclassi-cal techniques used in the description of gas phase reactions with biomolecular force fields used in molecular dynamics (MD) simulations. This leads to nonequilibrium MD simulations, which mimic the laser excitation of the molecules by nonequilibrium phase-space initial condition for the solute and the solvent atoms. This approach is based on the following assumptions. Firstly, it is assumed that an empirical force field at least provides a qualitative modeling of the process. This is because the initial relaxation appears to be an ultrafast and generic process and because it can be expected that the strong interaction with the polar solvent smoothes out many details of the intramolecular force field. Secondly, quantum-mechanical effects are only included via the nonequilibrium initial conditions of the classical simulations. This means that the method represents a short-time approximation of quantum mechanics. 

It is useful to point out that two sensitivity coefficients associated with parameters of the same type may give different sensitivities. For example, it is common in current biomolecular force fields to use the same force field parameter for chemically similar groups (e.g., the atomic partial charges for all the amide nitrogens have the same value in commonly used force fields such as those in the GROMOS, CHARMM, and AMBER molecular modeling packages). 

Kirschner, K.N., Yongye, A.B., Tsehampel, S.M., Gonzalez-Outeirino, J., Daniels, C.R., Foley, B.L., Woods, R.J. GLYCAM06 a generalizable biomolecular force field. Carbohydrates. J. Comp. Chem. 29, 622-655 (2008)... 

SIMULATED BINARY MIXTURE KIRKWOOD-BUFF INTEGRALS FOR POPULAR BIOMOLECULAR FORCE FIELDS A CASE STUDY... 

FIGURE 5.2 Comparisons of the excess coordination numbers for mixtures of methanol + water, benzene + methanol, N-methylacetamide + water, and zwitterionic glycine + water using the Kirkwood-Buff force field and the biomolecular force field that best reproduced the excess coordination numbers for each system. Please note the different y-axis scales. Error bars show the estimated standard deviation obtained from five 20-nanosecond subaverages. (See color insert.)... 

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