Sentence examples for minimization steps in from inspiring English sources

Each system was relaxed by 8000 minimization steps in NAMD (Phillips et al., 2005).

The initial molecular conformations for the adducts were subjected to a constrained energy minimization step in order to remove steric clashes.

The minimization step in each docking pose was performed with 1000 steps of the Steepest Descent and Conjugate Gradient.

Each ligand was minimized while binding to its target protein using the in situ ligand minimization module with the following parameters: CHARMm as an input force field, minimization algorithm as smart minimizer, maximum minimization steps equal to 1000, minimization with RMS gradient equal to 0.001 Å, and minimization energy change set equal to zero.

Minimization: protein solvation and minimization steps were performed using the Molecular Modeling ToolKit (MMTK) (15).

In particular, we guide the flux through the reactions in H as a result of minimizing flux in L and M. Note that the third-stage optimization is a path length minimization step, as is common in the literature [ 52].

In this latter minimization step, only BU99006 and residues having an atom within 3 Angstroms of Cys283 were left flexible, all others were fixed.

A Morse oscillator model was used to represent covalent bonding in the conjugate gradients minimization step, while a harmonic oscillator approximation was utilized for the steepest descents protocol.

In this step the binary files for the energy minimization step are prepared.

Next, we replaced six water molecules with sodium ions in order to neutralize the net negative charge of the system and repeated the energy minimization step.

An initial minimization step was performed for 6000 steps, followed by 20 ns of relaxation.