GRID calculation

It is usually recommended to test the results of 3-grid calculations with an additional fourth calculation to confirm the order of accuracy p and the extrapolated value,... 

The second step performs the GRID calculation with a given probe on the three subunit models. In order to make the application of Boolean operations with the map files as easy as possible, the matrix dimension of the GRID box is exactly maintained as in the largest model, i.e. that with a+fi subunits, maintaining, for both subunits, the original complex atom coordinates. The three maps obtained are named A, B and C, respectively (Fig. 7.1). 

Figure 3. Glucose K-factors (xL2/xL1) from VLLE measurements in the glucose+acetone+ water+carbon dioxide system against system temperature and pressure. ( = experimental data, grid = calculation results with Soave-Redlich-Kwong EOS, see text)...

Figure 3.4. Data collection for GRID/CPCA Starting from the GRID calculations for one probe, a one-dimensional vector containing all interaction energies at the k grid points is constructed. Then the vectors for the m probes are compiled into one long vector which contains (kx m) data points. The final X matrix is built by stacking these vectors for every target protein.

Claerbout, J. F., 1970, Coarse grid calculations of waves in inhomogeneous media with application to delineation of complicated seismic structure Geophysics, 35, 3, 407-418. 

Davis, M. E. and J. A. McCammon. (1990). Calculating Electrostatic Forces from Grid-Calculated Potentials. Journal of Computational Chemistry. 11 401-409. 

Figure IS. (a) Stereoview of the contour at —5 kcal/mol for the GRID calculation using a water probe (cyan) and the HIV-1 protease crystal structure [72]. Inhibitor 29 (yellow, first binding mode), an inserted water molecule (red), and Asp29 (magenta) are shown, (b) Stereoview of the contour at —5 kcal/mol for the GRID calculation using a water probe (cyan) and the HIV-l protease crystal structure [72]. Inhibitor 29 (yellow, second binding mode), an inserted water molecule (red), and Gly48 (magenta) are shown.

The horizontal arrows in Figures 1 and 2 correspond to contraction steps and, in typical Direct SCF calculations using PRISM, these account for a significant fraction of the total CPU time (15% in the pentacene run described in Section 4.7). In electrostatic grid calculations, the fraction is even higher. It is therefore very important that they be executed as efficiently as possible. 

We note, too, that things only improve under the fixed shell-pair scheme which is used in electrostatic grid calculations because the scalings become loop-invariants [98]. 

Yu, H.-G. An efficient grid calculation of vibrational states for H3 with geometric phase in hyper-spherical coordinates, Chem. Phys. Lett., 281 (1997), 312-318. 

Computation of the magnetic dipolar anisotropy. Generation of wave functions and plotting on spatial grids. Calculation of phonon spectrum. 

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