OPLS/AMBER

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

An alternative to the computationally intensive method of developing force fields from quantum mechanics has been to use empirical potentials, either transferable potentials that are meant to be used for many compounds (c.g OPLS, AMBER, TraPPE, etc.) or specialized potentials for specific compounds e.g., SPC, " TIP4P and later models for water). Such empirical potentials have been fit (frequently using simulation) to some experimental data. The results in Figure 7 for methanethiol illustrate the potential inaccuracies of using transferable potentials. There, we see that using a potential function fit to the quantum-mechanically... 

Some force fields for MM calculations on biomolecules (for example, OPLS, AMBER, CHARMM) exist in both united-atom (UA) and all-atom (AA) versions. A UA force field saves computational time by not explicitly including hydrogen atoms bonded to aliphatic carbon atoms. Instead, the field contains parameters for the CHj, CH2, and CH groups. 

Methods to determine the force-field parameters vary. Generally, bond lengths, angles and point charges are calculated by ab initio calculations, while the Lennard-Jones parameters and geometric force constants are taken from established sources such as OPLS, AMBER or CHARMM. 199,202 205 some cases, geometric force constants were also obtained from quantum cal-culations. Force-field parameters may be adjusted to available experimental data, although this was rarely found to be necessary. ... 

This is one of the simple and most commonly used method to perform multiscale simulation. By definition calculation of parameters for classical MD simulation from quantum chemical calculation is also a multiscale simulation. Therefore, most of the force filed e.g., OPLS," AMBER, GROMOS available for simulations of liquid, polymers, biomolecules are derived from quantum chemical calculations can be termed as multiscale simulation. To bridge scales from classical MD to mesoscale, different parameter can be calculated and transferred to the mesoscale simulation. One of the key examples will be calculation of solubiUty parameter from all atomistic MD simulations and transferring it to mesoscale methods such dissipative particle dynamics (DPD) or Brownian dynamics (BD) simulation. Here, in this context of multiscale simulation only DPD simulation along with the procedure of calculation of solubility parameter from all atomistic MD simulation will be discussed. 

In summary, MMFF represents a systematic attempt to combine the best features of such well-regarded force fields as MM3, OPLS, AMBER, and CHARMM into a single force field that is equally adept in small-molecule and macromolec-ular modeling applications. 

United Atom force fieldsare used often for biological polymers. In th esc m oleciiles, a reduced ii nm ber of explicit h ydrogen s can have a notable effect on the speed of the calculation. Both the BlOn and OPLS force fields are United Atom force fields. AMBER con tain s both aU nited and an All Atom force field. 

Lsc th e force fields th at have dern on strated accuracy for particu lar molecules or simulations. For example, CiPLS reproduces physical properties in liquid simulations extremely well. MM+ reproduces the structure and thermodynamic properties of small, nonpolar molecules better than AMBER, BIO+, and OPLS. 

Also use constant dielectric Tor MM+aiul OPLS ciilciilatimis. Use the (lislance-flepeiident dielecinc for AMBER and BlO+to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, n. can vary from 1 to H(l. IlyperChem sets tt to 1. .5 for MM-r. Use 1.0 for AMBER and OPLS. and 1.0-2..5 for BlO-r. 

AMBER. BlO-t-. and OPLS calciilations use information on atomic charges. Atomic charges can come from these sources ... 

Hach molecular mechanics method has its own functional form MM+. AMBER, OPL.S, and BIO+. The functional form describes the an alytic form of each of th e term s in th e poteri tial. For exam pie, MM+h as both a quadratic and a cubic stretch term in th e poten tial whereas AMBER, OPES, and BIO+ have only c nadratic stretch term s, I h e functional form is referred to here as the force field. For exam pie, th e fun ction al form of a qu adratic stretch with force constant K, and equilibrium distance i q is ... 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

HyperChem offers four molecular mechanics force fields MM+, AMBER, BIO+, and OPLS (see References on page 106). To run a molecular mechanics calculation, you must first choose a force field. The following sections discuss considerations in choosing a force field. 

The force field equations for MM+, AMBER, BIO+, and OPLS are similar in the types of terms they contain bond, angle, dihedral, van derWaals, and electrostatic. There are some differences in the forms of the equations that can affect your choice of force field. 

Note The BIO+ force field is an implementation of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field developed in the group of Martin Karplus at Harvard University. Like AMBER and OPLS, it is primarily designed to explore macromolecules. 

Another difference between the force fields is the calculation of electrostatic interactions. AMBER, BIO+, and OPLS use point charges to model electrostatic interactions. MM+ calculates electrostatic interactions using bond dipoles. The bond dipole method may not adequately simulate very polar or charged systems. 

AMBER, BIO-h and OPLS scale 1 van der Waals and 1 electrostatic interactions. Although the value of the 1 nonbonded scale factors is an option in HyperChem, you should generally use recommended values. This is because during parameterization, the force field developers used particular values for the 1 nonbonded scale factors, and their parameters may not be correct for other scale factors. 

The van der Waals scale factors used during force field parameterization are 0.5 for AMBER, 1.0 for BlO-t, and 0.125 for OPLS. Eor 1-4 electrostatic interactions, use 0.5 for AMBER, BlO-t, and OPLS. 

Choose the appropriate force field (MM-t, AMBER, OPLS, or BlO-t). 

Although interactions between vicinal atoms are nominally treated as nonbonded interactions, most of the force fields treat these somewhat differently from normal 1-5 and greater nonbonded interactions. HyperChem allows each of these nonbonded interactions to be scaled down by a scale factor <1.0 with AMBER or OPLS. For BlO-t the electrostatic may be scaled and different parameters may be used for 1 van der Waals interactions. Th e AMBER force field, for exam p le, norm ally u ses a scalin g factor of 0.5 for both van der Waals and electrostatic interactions. 

The OPLS atom types are a superset of the AMBER united atom types and the bonding parameters are just those of AMBER, supplemented where needed by the OPLS developers. The bond stretch, angle bending, dihedral angle and improper dihedral angle terms are identical to those of AMBER. Unlike AMBER, different combination rules are used for the van der Waals parameters, no hydrogen bonding term is used and no lone pairs are used. 

The OPLS form of electrostatic interactions is that of equation (26) on page 179. That is, it uses a charge-charge interaction just like AMBER. However, since the nonbonded potentials were developed... 

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