Sentence examples for mean force simulations from inspiring English sources

In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems.

The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities.

The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system.

To map out the nature of the active site dynamics we also utilize potential of mean force (PMF) simulations, where requisite degrees of freedom are held fixed (for example, a bond distance) while the remaining degrees of freedom are allowed to move.

Overall, this requires the execution of 5 to 30 simulations per interaction potential for IBI (each simulation using 16 128 cores), and 60 to 80 small simulations per interaction potential for calculating the potential of mean force (each simulation using a single core).

Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism.

(D ) Potential of mean force profile calculated from ABF simulations using the height of the D3 region (specifically the red sphere) as the reaction coordinate.

From the constrained simulations, the computed mean force between two carbon nanotubes in water exhibits a maximum at a tube spacing of 5.0 Å which corresponds to approximately one unstable layer of interstitial water molecules.

A first tertiary structure prediction for an S-layer protein (SbsB from G. stearothermophilus PV72/p2; Sára et al., 1996b) was obtained by molecular dynamic simulations using the mean force method (Horejs et al., 2008).

The landscape is mapped out by potentials of mean force derived from replica-exchange molecular dynamics simulations.

This mean force is generally obtained from restrained MD simulations by keeping the CVs relatively fixed in phase space.