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plot_ma <- function(d, start_lwd=0.9, start_gray=0.5, ...) {
  
  if(!is.data.frame(d))
    d <- as.data.frame(d)
 
  iter <- as.integer(floor(log(nrow(d), base=10)))

  dlwd <- (1.5 - start_lwd) / iter
  dgray <- (0.9 - start_gray) / iter
  pargs <- substitute(...)

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0 0
0.001 5.94285714285717e-05
0.002 0.000118857142857143
0.003 0.000178285714285715
0.004 0.000237714285714287
0.005 0.000297142857142859
0.006 0.00035657142857143
0.007 0.000416000000000002
0.008 0.000475428571428574
0.009 0.000534857142857146

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#the 3 is the number of frames in the trajectory to replay
variable i loop 3

#the stride is the time between frames 
variable stride equal 1

#set-up run here, including reading data/restart file
...
...
...

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{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {

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def stuff():
  print "Here"

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Prequisites: If you're on windows, you'll need to view file extensions. Go to the start menu and type Show or hide file extensions. The first search result will be a control panel setting for accomplishing this. There are checkboxes there. Make sure Show hidden files, folders, and drives is checked and Hide extensions for known file types is NOT checked.

Install Beautiful Soup 4. Type the command below in a command prompt (where you run ipython notebook)

conda install -c https://binstar.org/ioos beautifulsoup4

Install Mechanize:

conda install -c https://conda.binstar.org/dhirschfeld mechanize

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units lj #Lennard Jones - derived units
atom_style atomic #This says, we're using particles with interatomic forces

#THESE ARE MAGIC!
neighbor 1 bin
atom_modify map array sort 10 6


#-------------------------------------------------
#----------THESE COMMANDS SET-UP SIM BOX----------

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{
"A": 0.75, 
"R": 0.96, 
"N": 1.26, 
"D": 1.07, 
"C": 0.8, 
"Q": 0.83, 
"E": 0.80, 
"G": 1.47, 
"H": 0.96, 

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#set the font-size and size of things
figure.figsize: 5, 3
axes.labelsize: 14.3
axes.titlesize: 15.6
xtick.labelsize: 13
ytick.labelsize: 13
legend.fontsize: 13

grid.linewidth: 1.3
lines.linewidth: 2.275

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