View source for Code:MDIntro

# [http://pubs.acs.org/doi/pdf/10.1021/j100091a024 Water dimer structure]
# [https://spdbv.vital-it.ch/ Swiss PDB Viewer]
#* Download, extract to the default location (''C:\Users\<uname>\Downloads\SPDBV_4.10_PC''), and run spdvb.exe.
# Since sftp doesn't work from the lab computers, download files from [http://predictivestatmech.org/code/]
# Optional: compile and install [[Code:libxdrfile|libxdrfile]]
# Compute radial distribution functions using ''gmx rdf''
#*  gmx rdf -n ../index.ndx -f ../run.trr -o run.rdf.xvg
#* see [https://www.lehigh.edu/imi/teched/AtModel/Lecture_5_Micoulaut_Atomistics_Glass_Course.pdf]
# Compute P(r, theta)
#* see [https://docs.scipy.org/doc/numpy/reference/generated/numpy.histogram2d.html]

<source lang="python">
from xdrfile import xdrfile
from numpy import *

trr = xdrfile("../run.trr")

# create an empty histogram
H = zeros((500,500))
bins = 

# loop through frames
for frame in trr:
  print ( frame.x.shape)
  break
  # add this frame's histogram
  ## compute distances
  ## compute angles

# display/save histogram
H.save(

</source>