Sentence examples for using the parallel tempering from inspiring English sources

In particular we investigate six systems of three, four, six, eight, nine and twelve "Gly-Phe-Phe" (GFF) peptides at constant concentration and for eight different temperatures using the parallel tempering technique and with periodic boundary conditions (see Methods).

We performed simulations of six systems composed of three, four, six, eight, nine and twelve GFF three-peptides, using the parallel tempering technique [46] [47] using 8 temperatures ranging from T = 0.322 to T = 0.588 (Fig 1, Fig 2 and Fig 3).

For each system we calculate the free energy as a function of the inter-chain hydrogen bond interaction energy normalised over the number of peptides for each different temperature used in the parallel tempering.

Three repeated runs of a customized version of the parallel tempering MCMC algorithm presented in [ 37] are performed using ten temperature levels.

The parallel tempering (PT) scheme is employed to reduce the equilibration relaxation time of the composite system at a particular temperature ladder configuration in the SA process.

During the equilibration time, the parallel tempering procedure switched the ten evenly spaced temperatures with a probability of 0.05, corresponding to about once every twenty steps.

During the equilibration time, the parallel tempering procedure switched temperatures with a probability of 0.05, corresponding to about once every twenty steps.

After equilibration, the parallel tempering steps were all started from the same initial value, the maximum likelihood value found during the equilibration phase of the Monte Carlo procedure, and did not undergo any further switching between temperatures to ensure that the integration-over-temperatures interpretation of parallel tempering was valid.

The method is based on calculating, for each single system, the difference between the values of lnZ at two temperatures, using a Parallel Tempering procedure.

The same conclusion, namely an increase in kinase activity of the gatekeeper V561M variant, was independently reached using enhanced-sampling parallel tempering metadynamics molecular dynamics (MD) simulations (Fig. 3B and C).

All weights were determined using the Simulated Tempering Equal Acceptance Ratio (STEAR) method [7].