Sentence examples for sample simulations with from inspiring English sources

The mode selected is the one with largest amplitude in the case of both the control simulation (with no substrate) and the sample simulations with mannohexaose as substrate.

In this study, we carried out normal-mode analysis and enhanced sampling simulations with our recently developed method, molecular dynamics with excited normal modes, to understand the conformational equilibrium on these complexes.

In summary, we studied the entire dissociation processes of inhibitors from HIV-1 PR using the SMD simulations and umbrella sampling simulations with explicit water model.

Five series of umbrella sampling simulations (with different starting structures originating from unbiased QM/MM MD simulations) were performed.

This work presents an approach to reliability calculations in performance-based design, using an importance sampling simulation, with performance functions evaluated by localized interpolation of a response database.

Since the intention of the reserve allocation model is to cope with a serious emergency especially during peak load period, this paper used the non-sequential (state sampling) simulation with peak load.

The end point of the umbrella sampling simulation with the value of r corresponding to the highest point on each free energy surface (i.e., corresponding to the transition state) was used as the initial geometry for AM1/CHARMM22 potential energy calculations.

In the simulations with cellohexaose, the PCA mode representing the same movement was found to be only the mode with the third largest amplitude for two of the sample simulations and the mode with the fourth largest amplitude for the third sample simulation.

These initial windows were then used as starting points for umbrella sampling MD simulations with the pseudodihedral restraint.

For the sampling simulations, we began with a list of all non-duplicate interactions from the combined data set.

Preliminary umbrella sampling simulations were performed with the His523 Nε atom either protonated or unprotonated, to identify the most likely protonation state of this residue.