Sentence examples for minimization to remove from inspiring English sources

In fact, one can readily achieve lower-energy conformations of a given chemical structure by performing an all-atom energy minimization to remove any bond, angle, or torsion strain present in vacuo.

In the optimization stage, we initially used 5000 steps of conjugate gradient (CG) minimization to remove unfavorable contacts and ensure sufficient relaxation of the local environment near mutational site.

The solvated complex system were energy-minimized for 100 cycles of steepest-descent minimization followed by 100 cycles of conjugate-gradient minimization to remove close van der Waals contacts in the system, then heated from 0 to 300 K at a rate of 10 K/ps under constant temperature and volume, and finally simulated at 300 K under constant temperature and pressure.

This was followed by energy minimization to remove clashes, assignment of initial velocities from a Maxwell distribution, and 1 ns of solvent equilibration in which the positions of heavy protein and DNA atoms were restrained.

The top candidate model structures were refined via minimization to remove steric clashes and optimization of the hydrogen-bond network by means of side chain sampling using the Schrödinger's Maestro Protein Preparation Wizard [ 69].

The solvated system was subjected to energy minimization to remove the steric conflicts between atoms of protein and water molecules having a maximum step of 2000 with steepest descent integrator, that converge the energy when the maximum force was smaller than 1000 kJ·mol−1·nm−1.

Using the Schrödinger's Maestro software [ 75], each predicted 3D model was minimized, prepared, refined and re-minimized – minimization was used to remove steric clashes.

For minimization, a maximum of 5,000 steps using steepest descents [ 36] minimization was employed to remove bad van der Waals contacts.

100 conformations were generated followed by minimization and pruning to remove conformations that measure less than 0.25 Å away from each other in RMSD.

The steepest descent energy minimization was used to remove possible bad contacts from the initial structures until energy convergence reached 2,000 kJ/(mol.nm).nm

A maximum of 5,000 steps of steepest descents [ 44] minimization was employed to remove bad van der Waals contacts.