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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations

Fig. 2

Typical workflow and associated functions. The entire procedure can be divided into four tasks: 1) Extending the trajectory using the periodic boundary conditions and wrapping it around the unit cell of interest (Schemes 1 and 2). This is done by using two functions of the trajectory_utilities module, ExtendTrajectoryToNeighboringUnitCells and WrapTrajectoryInPeriodicCell; 2) Aligning the trajectory using the AlignTrajectoryOnFirstFrame function (Scheme 3). This function first calculates the density of the solvent from the first frame of the MD trajectory using CreateDensityMapFromEntityView and then aligns the trajectory using AlignTrajectoryOnDensity; 3) Calculation of tilts and splays, using AnalyzeLipidTiltAndSplay (Scheme 4). This function first calculates the water lipid interface, and the field of normal vectors on the surface by calling the GetBoundaryBetweenViews function. Then it calculates the lipid tilts and splays using AnalyzeLipidTilts and AnalyzeLipidSplays; 4) Obtaining the elastic moduli by using the ExrtactTiltAndSplayModuli function which calls FitTiltDistribution and FitSplayDistribution (Scheme 5)

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