įor this exercise, we will use three sets of data: Two (similar) peptides and a collection of butane molecules (You can get the files individually: ek12.psf ek12.dcd ck12.ps f ck12.dcd butane.psf butane.pdb butane.dcd j or everything as a. In addition, we can make movies using this data.
This gives us a powerful quantitative tool. These are usually binary (machine-readable), not ASCII (human-readable), as binary files are much smaller than ASCII, and all those coordinates add up! Having all these coordinates means that we are able to measure dynamic properties of our simulation experments: secondary-structure evolution, diffusion constants, correlations between groups, and so on. The common format we will use (from CHARMM and/or NAMD) is a. Thus, in order to get a (barely) meaningful simulation experiment of 10 ns, one would need 10 million timesteps of 1fs each.Įach trajectory file is essentially a PDB file for each saved timestep. In order to do this, time is broken up into discrete timesteps, usually 1 or 2 fs (1 fs = 10 -15 sec). What exactly is a step? Well, Molecular Dynamics integrates Newton’s equations, using the forces applied on each atom from its neighbors to move it around. Usually, not every finite time step of the simulation is saved: every 100 or 500 or 1000 steps saved is common. Trajectories are files that contain coordinates for all the atoms over the course of the simulation. Introduction to Molecular Dynamics Trajectories
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