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A Monte Carlo calculation is designed to generate static configurations of the system of interest, while molecular dynamics involves the solution of the classical equations of motion of the particles.
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Molecular dynamics involving extensive protein protein interactions, such as specific homodimerizations and heterodimerizations, as well as modular flexibility and posttranslational modifications, have been shown to determine the functional specificity of TFs.
The numerical simulation of many-particle systems (e.g. in molecular dynamics) often involves constraints of various forms.
The all-atom, multi-nanosecond molecular dynamics simulations involved the entire C-cadherin extracellular domain solvated in water (a 345,000 atom system).
Molecular dynamics simulations involving the sub-nanoscale interface reveal a most favourable set of temperature independent orientations of the monolayer graphene sheet with an angle of ∽15° between its armchair direction and [010] axis of the silicon substrate.
Molecular dynamics simulations involve many calculations of protein state evolution based on molecular entropy and are computationally costly.
The analysis of molecular dynamics trajectories often involves the comparison and clustering of thousands of snapshots.
The study presents a set of targeted molecular dynamics (MD) simulations involving selected complexes of the TRPM8 channel whose homology model was recently generated by some of us.
Our group is currently focusing primarily on long molecular dynamics (MD) simulations involving proteins and other biological macromolecules of potential interest from both a scientific and a pharmaceutical perspective.
Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential.
The work will involve molecular dynamics simulation of defects in polycrystals, graduate student Guoqiang Xu explained.
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