Reference no: EM133078894

Assignment

Your assignments for the Energy Landscapes and Molecular Dynamics sessions are to perform structural relaxations of a polymer strand and molecular dynamics simulations of a polymer in an implicit solvent, respectively. Please submit both together in a single pdf document that contains all plots, captions, and text.

Make sure that the quantities you report are converged with respect to the lengths of your equilibration and production runs. You will usually need to equilibrate for longer at low temperatures.

Your plots should be carefully and succinctly captioned and labelled so that the parameters of your simulations are made clear. You should include error bars where appropriate.

Assignment: Energy Minimization

Perform structural relaxations. Find the lowest potential energy you can for a 27-atom polymer.

Provide the following in your report:

1. One or two images of the final minimum-energy structure
2. The final values of U_bond, U_LJ, and U = U_bond + U_LJ in units of eV/atom.
3. One sentence which explains why the polymer adopts the shape that it does.

I don't care how you find the lowest energy structure. I have provided you with the crudest of steepest descent minimizers. This is perfectly adequate as long as you do relaxations from a large enough number of sufficiently-different ‘hot' starting structures. You can make each new hot starting structure by equilibrating at finite temperature with molecular dynamics for long enough to lose memory of the previous structure. This gives you a sufficiently-random ‘snapshot' structure, from which you can start a new minimization. In general, if you start each minimization from a very different structure, you start it in a different valley of the potential energy surface. The steepest descent algorithm finds the bottom of whatever valley you started in, but won't find minima in other valleys so you have to sample many starting points to have any chance of finding the ‘global minimum' (the deepest valley). If you wish, you can also implement a different minimization algorithm.

You can also try different step sizes for the steepest descent to optimize the speed of the relaxation (too small => too slow, too large => energy increases or the simulation crashes). One way to do this is to vary the value of timestep_factor in the code.

Play around with the code, doing many simulations to get a feel for what is happening, and then do whatever you can think of to find the lowest energy structure. The only thing you are not allowed to change is the set of parameters of the potential.

Attachment:- Energy Landscapes and Molecular Dynamics.rar