Sentence examples for during the md from inspiring English sources

All hydrogen bonds were constrained during the MD simulations using SHAKE algorithm.

Lennard Jones and electrostatic interaction energies between the ligand and its environment are gathered during the MD simulations.

The changes of target-ligand interaction energy (ELJ) and the RMSD during the MD stages in the Shaker protocol are plotted below the structural snapshots.

A two-dimensional heat transfer model was developed by coupling the latent heat, which is generated during the MD process, into the energy conservation equation.

Moreover, exploration of the conformational space of the systems during the MD simulation was carried out by a clustering data mining technique using the average-linkage algorithm.

The results were indicative of the stability of the model relating the observed structural changes during the MD simulation to the suggested ligand receptor interactions.

We analyzed the evolution of the contact surfaces during the MD simulations and investigated the frictional effects at the contact surfaces.

This unbound state in the crystal structure was also observed during the MD simulations.

Typically, the first few principal modes explain most of the motion observed during the MD simulation [20].

Time series of distance profiles monitoring PhC ligand binding during the MD simulations for the PDC109-PhC complex are shown in Fig. 3.

10.7554/eLife.11290.004 Figure 2. Inhibition of MMPs during the MD-period prevented adult OD-plasticity.