As a consequence, global mode calculations for the entire leading-edge region only need to include attachment-line structures.
Since DICTRA does not simulate the growth of needle-like precipitates, one has to set a mixed-mode calculation for a spherical-type of Mg2Si precipitate using the same value for the different parameters.
It's difficult to do mode calculations mentally for all but the smallest of datasets, so, in most cases, it's wise to begin by writing (or typing) your data set out.
Two modes of calculation for fitting five-membered ring conformations to 3J HH scalar coupling data obtained at up to five temperatures can be selected.
Enzymes catalyzing more than one reaction were considered with each reaction modeled independently in order to obtain a more accurate calculation for enzyme activity and convex base mode calculations (eg, glutaredoxin reactions 1 through 6).
Graphical summaries of the correlations coefficients for strands four to nine are shown in Fig. 2 and Supplementary fig. 3. Normal modes and trajectories of mode displacements were additionally calculated from the same structure used in the elastic normal mode calculations using GROMACS with the CHARMM27 force field combined with the OBC (Onufriev, Bashford, Case) implicit solvent model51.
Here, we call this series of calculations "iterative normal-mode calculation" and use this approach for forcing the conformational change of integrin from the bent to the extended forms and studying the role of the specific interactions in the conformational change.
The use of this approach allows one to reduce to twice the dimension of the nonlinear algebraic equations system for nonlinear normal modes calculations in comparison with systems obtained by previous researchers.
Occasionally, one wants to compute an integral that combines fields from two separate simulations (e.g. for nonlinear coupled-mode calculations).
Table 3 summarizes the data used for the DICTRA and the mixed-mode calculations.
Iterative normal-mode calculations showed that the spring needed to be eliminated for the conformational change.
