Soft-core potential

Here, avaw is a positive constant, and and ctJ are the usual Lennard-Jones parameters found in macromolecular force fields. The role played by the term avdw (1 — A)2 in the denominator is to eliminate the singularity of the van der Waals interaction. Introduction of this soft-core potential results in bounded derivatives of the potential energy function when A tends towards 0. 

As we have discussed in Sect. 2.8.5 a convenient approach to remedy this is to use soft-core potentials [55], in which the Lennard-Jones potential is replaced by... 

At the end of the chapter, techniques for alchemical transformations were presented. We showed that, in order to avoid rapid changes in free energy and improve the efficiency of the calculation, the parametrization of the Hamiltonian is critical and soft-core potentials should be used [see (4.50)]. A popular approach is the technique of A dynamics which leads to an improved sampling. In this approach A is a variable in the Hamiltonian system [see (4.51)]. Umbrella sampling, metadynamics or ABF can be used to reduce the cost of A dynamics simulations. 

Walls and Sternberg210 considered surface complementary for docking protein-protein complexes using a vdW-like soft core potential. The use of accessible surface area on binding and complexation has been discussed, for example, by Flower.205 Surface descriptors have been used to calculate solvation energies as part of the energetics of molecular association.144,188,211 Volume overlap was also used to quantify interactions of chemical compounds.201 The HINT exponential function and empirical atomic... 

The range of application of this idea can be extended by using soft-core potentials in reference simulations (34). A single perturbation formula does not work well when larger atoms or atomic groups are added or deleted because the... 

A generalization of the GCA to general pair potentials then follows in a natural way [19]. All interactions are treated in a unified manner, so that there is no technical distinction between attractive and repulsive interactions or between hard-core and soft-core potentials. This generalized GCA is most... 

We first generate the matrix elements of G as a function of co in a harmonic-oscillator basis, using the Reid soft-core potential [26] and the Barrett-Hewitt-McCarthy technique [27] as modified by Vary and Yang [28]. We repeat this calculation of G as the size of the 02p = 0 space... 

The results of these calculations for this rather simple system indicate that our proposed technique produces the sought for effects, i.e., an effective interaction of simple form that yields a reasonable numerical result in a tractable model space. The need to treat co as a variable parameter, in order to obtain the same result as an exact calculation for He using the same potential, indicates the known deficiencies in our calculations, such as the use of the Reid-soft core potential, instead of one of the more attractive meson-exchange potentials, and the lack of a self-consistent basis space. 

The result for the occupation number for k = 0 calculated according to (14) for the Reid soft core potential at kp = 1.36 fm" is 0.83. Results from other methods such as Brueckner theory [44,45]... 

Revalee, ).D., Laradji, M. and Kumar, P.B.S. (2008) Implicit-solvent mesoscale model based on soft-core potentials... 

Several methods have been proposed for reducing the intensity of repulsive interactions in this initial period, such as use of a cosine potential or a soft core potential.Unfortunately for both these forms the force is actually zero for r = 0 and there is still a finite chance of sites remaining superimposed. One method that has proved quite robust uses a truncated force potential in which the short-range force for neighbours i and j, where i -y > 5, is constrained to be constant below a critical separation rtr i.e.. 

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