Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide.
Glass WG., Essex JW., Fraternali F., Gebbie-Rayet J., Marzuoli I., Samways ML., Biggin PC., Khalid S.
Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.