Averaging Energetic Values

Quantities, which are selected from the Averages Only column and added to the Avg. graph column, will be written out and averaged, as described above, but will also be plotted on the molecular dynamics graph. To inspect the computed average value, select the quantity so that the outline appears around it and the average is displayed beside Value. 

HyperChem allows the computation and display of the potential energy (EPOT), the kinetic energy (EKIN), or the total energy ETOT = EPOT + EKIN. The temperature (TEMP) can also be chosen for averaging or plotting but is simply related to EKIN by EKIN = 3/2 NkTEMP. 

Eor free dynamics where the constant temperature check box in the Molecular Dynamics dialog box is not checked, the total energy ETOT should remain constant. A fluctuation of the total 

In addition to the energy quantities EKIN, etc., it is possible to average and plot their standard deviations D EKIN, etc. as described below. 

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Statistical mechanical averages in a molecular dynamics run are obtained by simply averaging an energetic or structural value over time steps. Thus if the values (xj, i are being computed in a trajectory. the statistical mechanical average is jiist... 

Moli cii lar dynamics is csscn Lially a sLiidy of ih c evniiitioii in tim c of energetic and siniclnral molecular data. The data is often best represented as a graph of a molecular quantity as a function of iime. The values to be plotted can be any qnantity x that is being averaged over the trajectory, or the standard deviation. Dx. You can create as many as four simultaneous graphs at once. 

Quantum numbers can be considered to be approximately equivalent to physical features in the atom proposed by Bohr. The principal quantum number corresponds to one of Bohr s circular energy shells. It is related to the average distance of the electrons from the nucleus. Electrons with larger n values are more energetic and farther from the nucleus. 

Once free energies of solvation are available, other solution properties can be determined, such as solute conformations, pKa values, electrode potentials, reaction energetics, etc.9 10 82 For example, Reynolds applied ab initio (HF and MP2) QM/MM approaches to computing the electrode potentials in water of a group of quinines 83 the average absolute deviations for the most stable conformations were 0.024 (HF) and 0.033 (MP2) volts, for a range of 0.322 volts. 

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