Snapshot, dynamics period

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. 

To create a set of snapshots of any molecular dynamics run, press the Snapshot button of the Molecular Dynamics Options dialog box to bring up the Molecular Dynamics Snapshots dialog box for naming a snapshot file. A snapshot file contains snapshots of the coordinates and velocities of a molecular system along the trajectory. The dialog box allows you to name the file and decide at what frequency to take snapshots. For example, choosing the snapshot period to be two data steps implies that only every other time step is stored in the snapshot file. 

Figure 6. Snapshot of the front shape with time step T/8 (from (a) to (d)), where T is the period of the front dynamics, for Vo — 0.5, U — 4.0 and L — 2n. Unburnt (burnt) material is indicated in white (black).

The molecular dynamics simulation was conducted at constant volume and constant temperature. Periodic boundary conditions, whereby a particle exiting the cell on one side is reintroduced on the opposing side with the same velocity were imposed. Constant temperature conditions were implemented through simple velocity rescaling. The probability to rescale atom velocities was chosen to be 0.1 per time step. A dynamic time-step of 0.5 fs was used, and snapshots at 2.5 fs steps were collected. 

QM/EFP methods were applied to understand solvent effects and relaxation dynamics of the CT state of pNA in three different solvents water, dioxane, and cyclohexane [57], Specifically, pNA was described by the configuration interaction singles with perturbative doubles [C1S(D]] method [92] in 6-31-t-G basis, while solvent molecules were represented by the EFP fragments. For each system, pNA molecule was solvated by 64 solvent molecules. Configurational space of each system was sampled with EFP MD (in which pNA was also represented as an EFP fragment) with periodic boundary conditions, using NVT ensemble at 300 K. Snapshots from the... 

Figure 4 Shadowgraph snapshots of the dynamical shape changes in the oscillatory regime. Arrows point in the direction of the main swellingdeswelling dynamics. Snapshots from (a) to (f) at 0, 20, 30, 40, 44, 00 minutes, cover about one period of oscillation of the mid-heigth point of the gel Experimental conditions d=0.5mm, [OH ]o=4-25xlO M. White scale bar in (a)=3mm.

Figure 12. Snapshot from an 85 ps molecular dynamics simulation of Shorthorn sculpin in a periodic box of waters.

We represented receptor flexibility by utilizing several snapshot from molecular dynamics (MD). The MD simulations were performed with the software YASARA Structure 15.6.21. We used AMBER03 as force field with long-ranged PME potential and a cutoff of 8.0 A. The starting structures for the simulations of the ARs were extracted from the X-ray structures from the PDB database. A cubic periodic simulation cell of 512000 A was defined around all atoms of the receptor structures. The MD simulation was then initiated at 298 K and integration time steps for inffamolecular forces every 1.25 fs. 

Figure 1. (a) Snapshot of the model system containing four graphite sheets, two PF ions, and ten Li+ ions spheres), solvated in 69 propylene carbonate and 87 ethylene carbonate molecules after reaching constant volume in the NPT ensemble, (b) Snapshot after 200 ns molecular dynamics simulation. The ensemble is the NVT ensemble. The system has periodic boundary conditions and is simulated at 1 atm and 300 K. Top view, perpendicular to the plane of the graphite sheets. 

---