Sentence examples for constraining bond from inspiring English sources

Amber99 can be written as a linear combination of six terms E s = E bs + E ab + E it + E ta + E vdw + E cc, where E bs, E ab, E it and E ta are the bonded terms constraining bond lengths, bond angles, improper torsion angles and torsion angles, respectively.

The Particlemesh Ewald method for long-range electrostatics, a 14 Å cutoff for van der Waals interactions, a 12 Å cutoff for Coulomb interaction with updates every 2 steps, and the SHAKE algorithm to constrain bond lengths were used28.

The LINCS algorithm [31] was used to constrain bond lengths and angles.

The LINCS algorithm was used to constrain bond lengths (43).

SHAKE algorithm was used to constrain bond lengths involving hydrogen [ 13].

SHAKE algorithm was used to constrain bond lengths involving hydrogen, permitting a time step of 2 fs.

The LINCS algorithm was used to constrain bond lengths in both the lipid molecules and the protein.

Note that no restraints, other than the LINCS algorithm that constrains bond lengths, were imposed during the production AT-MD simulations.

The commonly used SHAKE algorithm and particle-mesh Ewald (PME) method are used to constrain bond lengths involving hydrogen atom(s) and in the calculation of long range electrostatic forces, respectively.

The SHAKE algorithm48 was used to constrain bonds involving hydrogen atoms.

The SHAKE procedure, which weakly constrains bonds involving hydrogen atoms, was applied to each step of the simulation.