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--- exercises:2019_conexs_newcastle:ex4 [2019/09/11 03:50] – [Part 2: MD of liquid water] abussy
+++ exercises:2019_conexs_newcastle:ex4 [2019/09/11 13:12] – [Part 2: MD of liquid water] abussy
@@ Line 298: / Line 298: @@
 &END TOPOLOGY
 </code>
-where we specify the filename, format, and that we should not divide our atoms into molecules. When you have finished running the above input, try to use the following python script to convolve your spectra with Gaussian functions. Note that you might have to change the parameters at the top of the file to get pleasing results. If a new window with the plot does not open, it is also saved in the current directory as "pdos.png".
+where we specify the filename, format, and that we should not divide our atoms into molecules. When you have finished running the above input, try to use the following python script to convolve your spectra with Gaussian functions. You do this by first loading Python3 by typing
+<code>
+module load Anaconda3/5.0.1
+</code>
+and then typing
+<code>
+python pdos_conv.py
+</code>
+Note that you might have to change the parameters at the top of the file to get pleasing results. If a new window with the plot does not open, it is also saved in the current directory as "pdos.png".
 <code - pdos_conv.py>
 import numpy as np
-import matplotlib.pyplot as plt
 import os
+import matplotlib as mpl
+mpl.use('Agg')
+import matplotlib.pyplot as plt
 # Parameters
@@ Line 411: / Line 421: @@
     * liquid_water-pos-1.xyz - containing your trajectory
 Examine liquid_water-1.ener and make sure that the temperature and total energy remains reasonably stable during the run. As a final exercise, use a slightly modified python code from Part 1 to see how the PDOS spectrum changes with time.
-<code - asdas.py>
+<code - pdos_conv_md.py>
 import numpy as np
-import matplotlib.pyplot as plt
 import os
+import matplotlib as mpl
+mpl.use('Agg')
+import matplotlib.pyplot as plt
 # Parameters