Sentence examples for generalized solvent from inspiring English sources

The resulting potential energy is a function of the generalized solvent coordinate and the change in the A O distance.

Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB).

We thus generated a reference ensemble of the GB1 domain using an MD simulation with the CHARMM22 topology format and force-field [42] with a modified backbone potential [43] and a generalized Born solvent model [44].

The generalized Born solvent model was used for simulated annealing, with a salt concentration of 0.2 mM (33, 34).

Molecular dynamics simulations were performed with AMBER11 [ 60] and the GLYCAM06 force field [ 61] in an implicit generalized Born solvent.

The generalized Born solvent model was used with a salt concentration of 0.1 M, and the SHAKE algorithm was used (44, 45).

Solvent was simulated with the generalized Born implicit solvent model and 0.1 M NaCl.

Use of simplified energy function that takes into account the backbone conformational and side-chain interaction preferences observed in the experimental RNA structures [ 56 ], AMBER force field [ 57 ], and generalized Born implicit solvent [ 58 ] helps generalize the technique.

The ff99sb calculations were performed with the generalized Born implicit solvent model, and the PM6 and PM6-DH2 calcusedions used the COSMO solvent model in MOPAC.

The magnitudes and signs of the various components are estimated from the AMBER parm94 force field, generalized Born theory, solvent accessibility measures, and empirical estimates of quantities related to ion release.

The generalized Born implicit solvent model [23], [24] was used to model the effects of solvation.