Sentence examples for by using umbrella sampling from inspiring English sources

Other studies have probed the energetic characteristics of localized backbone degrees of freedom individually by using umbrella sampling [23] or unrestrained [24] MD simulations.

To gain more insight into the lack of pocket opening events, we estimated the free energy for opening by using umbrella sampling 23 to bias the side-chain of Tyr481 to sample different χ1 torsion angle values.

Subsequently, we calculated the free energy profile along the identified ion permeation path for a single Na+ ion using umbrella sampling (US) (see Supplementary Materials for details).

The free-energy profile for the position of the syb2 membrane anchor in the membrane was determined using umbrella sampling.

We demonstrate the feasibility of using "umbrella sampling" to do Monte Carlo Markov-sampling runs each covering a substantial range of density: "density-scaling Monte Carlo," or DSMC.

The PMF for the binding of the [Lys]-fullerene to the NavAb and Kv1.3 channels is determined using umbrella sampling with this equilibrated structure.

The binding affinities between the inhibitor and Aβ as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations.

The procedure for calculation of the free energy of base flipping using umbrella sampling with the previously described pseudodihedral coordinate [17] is slightly modified in this study.

First, we needed to locate the minimum for the intermediate state by varying the distance between the diphosphate anion and the carbocation of the prenylation product using umbrella sampling.

When using umbrella sampling [ 80, 81] and the weighted histogram method [ 82] for the blue moon ensemble approach, the free energy is estimated from the reaction coordinates.

In this study, the intrinsic energetic differences in unstacking among these three cytosines in a solvated DNA duplex overhang model were examined using umbrella sampling molecular dynamics simulations.