Equilibration and Data Collection

In many molecular dynamics simulations, equilibration is a separate step that precedes data collection. Equilibration is generally necessary to avoid introducing artifacts during the heating step and to ensure that the trajectory is actually simulating equilibrium properties. The period required for equilibration depends on the property of interest and the molecular system. It may take about 100 ps for the system to approach equilibrium, but some properties are fairly stable after 10-20 ps. Suggested times range from 5 ps to nearly 100 ps for medium-sized proteins. 

Equilibration corrects the velocities of atoms. Velocities resulting from heating do not simulate the type of motion found in a real molecular system. Instead, these velocities depend on a random distribution of values corresponding to a given temperature and on the forces in a partially minimized structure. 

To generate characteristic velocities and bring a molecular system to equilibrium at the simulation temperature, atoms are allowed to interact with each other through the equations of motion. Eor isothermal simulations, a temperature bath scales velocities to drive the system towards the simulation temperature. Scaling occurs at each step of a simulation, according to equation 28. 

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A rn uleculur dynam ics si in illation can li ave tli rcc distinct time and teiTi pcratii re periods h eating, simulation (niri). an d eoolin g. If yon wan t to meast re equilibrium properties of a molectilar system. yon can divide til e sitn 11 lation period into two parts equilibration and data collection. ... 

To reach equilibrium temperature quickly before starting the equilibration phase of a simulation (see Equilibration and Data Collection on page 74). 

Amolecular dynamics simulation can have three distinct time and temperature periods heating, simulation (run), and cooling. If you want to measure equilibrium properties of a molecular system, you can divide the simulation period into two parts equilibration and data collection. 

In our system the data collection process is essentially a passive slave to the chromatograph, which is controlled by its own internal microprocessor. An amplifier matches the voltage output from the strip chart recorder terminals on the chromatograph to the A/D converter input. The data collection program uses the "Equilibration Pulse" and "Injection Pulse" relay closures shown in Figure 1 to synchronize the data collection process with the operation of the autosampler on the chromatograph. 

Fig. 2.12. Enthalpy, entropy, and free energy differences for the ethane —> ethane zero-sum alchemical transformation in water. The molecular dynamics simulations are similar to those described in Fig. (2.7). 120 windows (thin lines) and 32 windows (thick lines) of uneven widths were utilized to switch between the alternate topologies, with, respectively, 20 and lOOps of equilibration and 100 and 500 ps of data collection, making a total of 14.4 and 19.2 ns. The enthalpy (dashed lines) and entropy (dotted lines) difference amount to, respectively, —0.1 and +1.1 kcalmol-1, and —0.5 and +4.1 calmol-1 K For comparison purposes, the free energy difference is equal to, respectively, +0.02 and —0.07kcalmol I, significantly closer to the target value. Inset Convergence of the different thermodynamic quantities...

Both FEP and TI are carried out by systematically varying X from the initial state 0 to the final state 1. At each X point, equilibration of the system is performed, followed by data collection to determine the value of the ensemble for the equilibrated system. 

The free energy perturbation calculations on mutation of the central statine residue of pepstatin to its dehydroxy and other derivatives were carried out using the window method. The crystal structure reported by Suguna et al.l4 l5was used for these calculations. In most simulations, the mutations were achieved either in 101 or 51 windows with 0.4 ps of equilibration and 0.4 ps of data collection at each window. The calculation for each mutation was repeated in water to determine the difference in the free energies of solvation and to complete the thermodynamic cycle. 

Figure 2). The calculations were done in the microcanonical ensemble at a temperature of 300K 5K. Energy was well conserved throughout the trajectories, and no overall drifts in molecular temperature were observed. Small ensembles of trajectories (12 for SI and 6 each for the other minima) were calculated for the averaging of system properties. Each trajectory was equilibrated by velocity reassignments during an initial period of 20ps, followed by another 20ps of dynamics used for data collection.

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