Sentence examples for molecular dynamics protocol from inspiring English sources

The objective of this research is to develop a molecular dynamics protocol to examine the interaction between drugs and formulations at the atomic level.

We describe a molecular dynamics protocol that integrates PGHS monomers into phospholipid bilayers, thereby producing in silico atomistic models of the PGHS system.

The interaction energies given in Figure 3 must be interpreted with care: the standard molecular dynamics protocol used here does not reflect atom polarizability [27], [28].

The following molecular dynamics protocol was applied to each system: In a 1.5 pico-seconds (psec) heating phase the temperature was raised to 300 K in steps of 10 K over 0.05 psec blocks.

All molecular dynamics simulations were performed using GROMACS version 3.3.1, 4.0, or 4.5 and followed the same molecular dynamics protocol that was described in our previous work.

First, the relaxation time of almost 20 ns (including time used for the equilibration period of the molecular dynamics protocol) is likely long enough for sufficient local relaxation of the initial geometry adopted.

This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes.

Proper energy minimisation is routinely performed in the subsequent molecular dynamics simulation protocol (we used a steepest-descent method).

Structures were calculated using the simulated annealing molecular dynamics refinement protocol within the program XPLOR-NIH [ 43].

On the basis of this rescoring protocol we tested several molecular dynamics simulation protocols in combination with different MM-PBSA, and MM-GBSA calculation procedures using Amber 10 [2] and Gromacs 4 [3].

Amber (Case et al. 2002) force field solution structures of I were generated by free molecular dynamics using the protocols described in the Material and methods.