Molecular dynamics averages

I o averageu torsion, select the fouratoms of the torsion, name the torsion tor, for exam pie, and then select tor as Lh e quan tity Lo be averaged from the Molecular Dynamics. Averages dialog box. 

Averages or plotted values at regular time intervals. You specify an Average/Graph period in the Molecular Dynamics Averages dialog box. 

You choose the values to average in the Molecular Dynamics Averages dialog box. As you run a molecular dynamics simulation, HyperChem stores data in a CSV file. This file has the same name as the HIN file containing the molecular system, plus the extension. CSV. If the molecular system is not yet stored in a HIN file, HyperChem uses the filename chem.csv. 

To average or plot a structural quantity, the structural quantity must first be selected and named by the normal process for creating named selections (select the atoms and then use the menu item Select/Name Selection to give the selected atoms a name). Erom then on the Molecular Dynamics Averages dialog box will show these named selections as possible candidates to be averaged or plotted in addition to energetic quantities described above. 

The single average value that is reported for this quantity in the Molecular Dynamics averages dialog box is the limit reached by the plotted values at i=N, i.e. the RMS value of x ... 

S. K. Schiferl and D. C. Wallace, Statistical Errors in Molecular Dynamics Averages, J. 

Figure 61. Positional error in refinement of the 25-ps data from myoglobin simulation The deviations between atomic positions are calculated after the molecular dynamics average structure and the refined structures are superimposed by least squares. The deviations for backbone atoms (N, C, and C", solid line) and sidechain atoms (dotted line) are averaged over residues.

Arizumi, N., Bond, S. On the estimation and correction of discretization error in molecular dynamics averages. Appl. Numer. Math. 62, 1938-1953 (2012). doi 10.1016/j.apnum.2012. 08.005... 

While the calculation of the properties of matter by ensemble methods has attained preeminence in statistical mechanics, nonetheless the method of time averages along a dynamical trajectory is no less fundamental a technique to determine such properties. We define then the molecular dynamics average of a phase function /(x ) as... 

Hiese can be calculated for t not too large by the Monte Carlo-molecular dynamics averages... 

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