Sentence examples for solvent box from inspiring English sources

This peptide-SDS ensemble was then minimized in an aqueous solvent box with Hyperchem 7.5, using the CHARMM 27 option (see Methods).

This created a solvent box with dimensions of approximately 40 Å by 50 Å by 120 Å and approximately 110,000 atoms (See Figure 4a b).

This peptide-SDS ensemble was then minimized in an aqueous 56 Å3 solvent box with sodium counter ions for electronic neutrality with Hyperchem 7.5, using the CHARMM 27 option [77].

The homology structures for MB and S-MB were each placed in a periodic 65 cubic Å box of HFIP∶spc water (4∶6, v∶v) to emulate the solution environment of the FTIR measurements (equilibrated HFIP solvent box and topology files courtesy of D. Roccatano) [71].

These structures were placed in a periodic 56 Å3 box of TIP4P water or HFIP TIP4P water (4∶6, v:v) and the ensemble was neutralized with counter-ions to simulate the environment used for our CD measurements (equilibrated HFIP solvent box and topology files courtesy of D. Roccatano) [73].

Chloride counterions were added to the solvent box with the peptide to neutralize its charge with constraints on the peptide; the ensembles were then subjected to 100 psec of MD at 300K using the ffG53a6 force field option that allows the solvent to equilibrate while restraining the peptides.

Typically, users may have equilibrated "solvent boxes" which have been run for long simulations to ensure proper density, and both short and long-range interactions between solvent molecules.

Using such solvent boxes allows placing solute molecules, such as proteins, in an approximately correct initial structure, such as that shown in Figure 13.

The calculation was run in vacuum without any solvent or periodic box.

(B ) Calcium signals of ROI 3 (x-axis) and ROI 4 (y-axis) (% norm ΔF/F, separated by axes) in response to odor stimulation (colored boxes) and the solvent mineral oil (grey box).

All simulations were carried out in implicit solvent, given the high box dimensions that would be needed for such elongated structures.