Code:MDIntro

1. Water dimer structure
2. Swiss PDB Viewer
   • Download, extract to the default location (C:\Users\<uname>\Downloads\SPDBV_4.10_PC), and run spdvb.exe.
3. Since sftp doesn't work from the lab computers, download files from [1]
4. Optional: compile and install libxdrfile
5. Compute radial distribution functions using gmx rdf
   • gmx rdf -n ../index.ndx -f ../run.trr -o run.rdf.xvg
   • see [2]
6. Compute P(r, theta)
   • see [3]

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

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

1. create an empty histogram

H = zeros((500,500)) bins =

1. loop through frames

for frame in trr:

 print ( frame.x.shape)
 break
 # add this frame's histogram
 ## compute distances
 ## compute angles

1. display/save histogram

save("H.npy", H)

</source>