# Open SourceMolecular Dynamics

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exercises:2018_ethz_mmm:h2o_md

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 exercises:2018_ethz_mmm:h2o_md [2018/03/02 11:01]dpasserone exercises:2018_ethz_mmm:h2o_md [2018/03/02 15:36] (current)dpasserone Both sides previous revision Previous revision 2018/03/02 15:36 dpasserone 2018/03/02 14:58 dpasserone 2018/03/02 14:57 dpasserone 2018/03/02 11:14 dpasserone 2018/03/02 11:13 dpasserone 2018/03/02 11:01 dpasserone 2018/03/02 05:48 dpasserone 2018/03/02 05:25 dpasserone created Next revision Previous revision 2018/03/02 15:36 dpasserone 2018/03/02 14:58 dpasserone 2018/03/02 14:57 dpasserone 2018/03/02 11:14 dpasserone 2018/03/02 11:13 dpasserone 2018/03/02 11:01 dpasserone 2018/03/02 05:48 dpasserone 2018/03/02 05:25 dpasserone created Line 9: Line 9: Download the 2.1 exercise into your **EXERCISES** folder and unzip it. Download the 2.1 exercise into your **EXERCISES** folder and unzip it. - <​code>​ + - max@qmobile:​~$cd ; cd EXERCISES + - max@qmobile:​~$ wget https://​polybox.ethz.ch/​index.php/​s/​ULaq6rjhg4Pu63A + - max@qmobile:​~$unzip exercise_2.1.zip + - max@qmobile:​~$ cd exercise_2.1 + - ​ + This exercise is mostly taken by a [[https://​www.cp2k.org/​exercises:​2015_uzh_molsim:​index|previous lab session]] by Marcella Iannuzzi, UZH, who should be credited and acknowledged here. This exercise is mostly taken by a [[https://​www.cp2k.org/​exercises:​2015_uzh_molsim:​index|previous lab session]] by Marcella Iannuzzi, UZH, who should be credited and acknowledged here. Line 244: Line 239: - Run the **md300.in**:​ the command is <​code>​cp2k.ssmp -i md300.in > md300.out ​ - Run the **md300.in**:​ the command is <​code>​cp2k.ssmp -i md300.in > md300.out ​ - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function - - Extract the diffusion coefficients and compare the two approaches:​ + - Extract the diffusion coefficients and compare the two approaches ​(the instruction about the parameters: **./​command.py -h**) - <​code>​vel_autocorr.py T300-vel-1.xyz 3 10 100 + <​code>​./vel_autocorr.py T300-vel-1.xyz 3 10 100 - vel_autocorr_plot.py vel_autocorr.out + ./vel_autocorr_plot.py vel_autocorr.out - mean_square_displ.py T300.xyz 3 10 100 + ./​mean_square_disp.py T300.xyz 3 10 100 - msd_fit_and_plot.py mean_square_disp.out + ./msd_fit_and_plot.py mean_square_disp.out ​ - + Remember: to display the **png** files, the command is <​code>​display file.png​ + ​Assignments + - look at the file T300-1.ener at the end of the simulation. It contains several quantities. Check the header! + - Using gnuplot, check the stability of the MD, you can also use <​code>​ ./​simpleplot.py Col1 Col2 ​ + - How do you interpret the oscillation of the potential energy? And of temperature?​ + - Compare the values of the diffusion coefficient with the two methods. Are they compatible? + - Look at the trajectories with vmd. Why are the particles "​exiting"​ the box with time? What is the importance of this for the algorithm?​ + - Copy md300.in into md200.in and change the system name and the initial temperature. Run the md. What is the final temperature?​ Why? + - Copy md300.in into md400.in and change to 400 in the two places. Run the md. What is the final temperature?​ Why? + - Check the temperature dependence of the diffusion coefficient. Plot the result.