Van der Waals parameters

Once the molecules are aligned, a molecular field is computed on a grid of points in space around the molecule. This field must provide a description of how each molecule will tend to bind in the active site. Field descriptors typically consist of a sum of one or more spatial properties, such as steric factors, van der Waals parameters, or the electrostatic potential. The choice of grid points will also affect the quality of the final results. 

Because of the restricted availability of computational resources, some force fields use United Atom types. This type of force field represents implicitly all hydrogens associated with a methyl, methylene, or methine group. The van der Waals parameters for united atom carbons reflect the increased size because of the implicit (included) hydrogens. 

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. 

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... 

The van der Waals parameters of the metal in a liganded site may be significantly... 

Each of the 71 atom types has two van der Waals parameters, and giving 142 parameters. 

Density matrix element in AO basis Matrix eigenvalue van der Waals parameter Dielectric constant... 

The approach taken above estimates the effect of the metal by simply considering its electrostatic effect (subjected, of course, to the correct steric constraint as dictated by the metal van der Waals parameters). To examine the validity of this approach for other systems let s consider the reaction of the enzyme carbonic anhydrase, whose active site is shown in Fig. 8.6. The reaction of this enzyme involves the hydration of C02, which can be described as (Ref. 5)... 

The temperature-independent van der Waals parameters a and b are unique for each gas and are determined experimentally (Table 4.5). Parameter a represents the role of attractions so it is relatively large for molecules that attract each other strongly and for large molecules with many electrons. Parameter b represents the role of repulsions it can be thought of as representing the volume of an individual molecule (more precisely, the volume per mole of molecules), because it is the repulsive forces between molecules that prevent one molecule from occupying the space already occupied by another molecule. 

Calculate the apparent volume (in pnt1) and radius (in pm) of a helium atom as determined from the van der Waals parameters,... 

Show that the van der Waals parameter b is related to the molecular volume um() by b = 4NAumn. Hint. Treat the molecules as spheres of radius r, so that unlH = nr5. The closest that the centers of two molecules can approach is 2r. 

Here, q, stands for the net atomic charge borne by atom i. R 3 and sl3 are the van der Waals parameters for the pair of atoms, j and the superscripts (1) and (0) refer, respectively, to the target and the reference states. Clearly, this is just one example of how modifications of the Hamiltonian can be handled. To optimize performance of FEP simulations, one might use several order parameters in... 

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