# Open SourceMolecular Dynamics

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exercises:2017_ethz_mmm:pythonmd

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 exercises:2017_ethz_mmm:pythonmd [2017/03/03 05:55]dpasserone exercises:2017_ethz_mmm:pythonmd [2017/03/03 16:38] (current)dpasserone Both sides previous revision Previous revision 2017/03/03 16:38 dpasserone 2017/03/03 16:37 dpasserone 2017/03/03 11:03 dpasserone 2017/03/03 05:55 dpasserone 2017/03/03 05:54 dpasserone 2017/03/03 05:50 dpasserone 2017/03/03 05:48 dpasserone 2017/03/03 05:26 dpasserone 2017/03/03 05:25 dpasserone 2017/03/03 04:47 dpasserone 2017/03/02 16:14 dpasserone 2017/03/02 15:16 dpasserone created Next revision Previous revision 2017/03/03 16:38 dpasserone 2017/03/03 16:37 dpasserone 2017/03/03 11:03 dpasserone 2017/03/03 05:55 dpasserone 2017/03/03 05:54 dpasserone 2017/03/03 05:50 dpasserone 2017/03/03 05:48 dpasserone 2017/03/03 05:26 dpasserone 2017/03/03 05:25 dpasserone 2017/03/03 04:47 dpasserone 2017/03/02 16:14 dpasserone 2017/03/02 15:16 dpasserone created Line 5: Line 5: - All files of this exercise be downloaded from the wiki: {{e2.zip|}} ​ + All files of this exercise be downloaded from the wiki: {{e2_bis.zip|}} ​ Download the exercise into your $HOME folder and unzip it. Download the exercise into your$HOME folder and unzip it. <​code>​ <​code>​ - you@eulerX ~$wget http://​www.cp2k.org/​_media/​exercises:​2017_ethz_mmm:​e2.zip + you@eulerX ~$ wget http://​www.cp2k.org/​_media/​exercises:​2017_ethz_mmm:​e2_bis.zip - you@eulerX ~$unzip exercises:​2017_ethz_mmm:​e2.zip + you@eulerX ~$ unzip exercises:​2017_ethz_mmm:​e2_bis.zip you@eulerX ~$cd exercise_2 you@eulerX ~$ cd exercise_2 ​ Line 112: Line 112: prints=“False”​ prints=“False”​ execute three or four times the program and write down the execution time that you get as the only output. execute three or four times the program and write down the execution time that you get as the only output. - Now comment the lines for the “efficient” algorithm and uncomment the lines of the ”unefficient” one. Execute ​with 3-4 different timesteps. + Now comment the lines for the “efficient” algorithm and uncomment the lines of the ”unefficient” one. Execute 3-4 times. Is the execution time longer? Why do you think you get such a result? Is the execution time longer? Why do you think you get such a result? Line 162: Line 162: -  What is the value of the total energy? Is it conserved? -  What is the value of the total energy? Is it conserved? -  Increase the time step to 3 fs, and run it again. What happens to the total energy? -  Increase the time step to 3 fs, and run it again. What happens to the total energy? + - Note: to visualize a trajectory you can use the code (look inside it!) traj.py in the directory: + <​code>​python traj.py​ + + ​Here an example of [[http://​users.mccammon.ucsd.edu/​~dzhang/​energy-unit-conv-table.html|energy conversion table]].