Dialog averaging

Snapshots at regular time intervals that store atomic coordi-riaies and velocities. You can play back these snapshots to inspect the simulated structures or to average values. Yon specify a Snapshot period in the Molecular Dynamics Snapshots dialog box. 

You ch oosc Ih c viilucs Lo avcriigc iii Ih e Molten kir Dynamics Averages dialog hox. As you run a molecular dynamics simulaLion, IlyperChem stores data m a CSV lile. This file has the same name as the IIIN file containing the molecular system, plus the extension. fov. If the molecular system is not yet stored in a IIIX file, IlyperChem uses the filename chem.csv. 

Before startiu g a in olecular dyri am ics simulation, L-click on Averages in the Molecular Dynamics Option s dialog box. 

I o sorn c ex ten t you can rn on itor eon stan t tern peratii re sim ula-tion s by th e tern perature (I KMP) an cl its deviation (D TKM P) or by kinetic en ergy (KKIN) an d its deviation (D HKIN). Plot th ese values using the HyperChem Molecular Averages dialog box. 

HyperChem run s the molecular dynain ics trajectory, averaging and analyzing a trajectory and creating the Cartesian coordinates and velocities, fhe period for reporting these coordinates and velocities is th e data collection period. At-2. It is a m iiltiplc of the basic time step. At = ii At], and is also referred to as a data step. The value 1I2 is set in the Molecular Dynamics options dialog box. 

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. 

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

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

To some extent you can monitor constant temperature simulations by the temperature (TEMP) and its deviation (D TEMP) or by kinetic energy (EKIN) and its deviation (D EKIN). Plot these values using the HyperChem Molecular Averages dialog box. 

HyperChem includes a number of time periods associated with a trajectory. These include the basic time step in the integration of Newton s equations plus various multiples of this associated with collecting data, the forming of statistical averages, etc. The fundamental time period is Atj s At, the integration time step stt in the Molecular Dynamics dialog box. 

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. 

Add error bars to the averages plotted, using as before the Format Data Series dialog box, where you select theY Error Bars tab, then specify the Error Amount under Custom as =AVERAGE F3 F302 in both directions, and compare with Fig. 2.2-4. 

On average, costs for DIALOG data bases run between 65.00- 120.00 for an hour of on-line connect time. 

Figure 10.58 a The Averaging dialog box files to average are selected by symbols, b The Averaging dialog box files to average are selected by names. 

Table 1. Average time to perform the gesture for closing the dialog in the first task...

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