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exercises:2018_ethz_mmm:pmf

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exercises:2018_ethz_mmm:pmf [2018/05/25 11:13]
dpasserone
exercises:2018_ethz_mmm:pmf [2018/05/25 14:19]
dpasserone
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   - Directories R_<​distance>​ will be created (check with ** ls -ltr ** )   - Directories R_<​distance>​ will be created (check with ** ls -ltr ** )
   - You can enter a certain directory (e.g., R_12.5), check the **log.lammps** for the evolution of a trajectory, and visualize the trajectory with: **vmd mol_sub.xyz trajectory.dcd**   - You can enter a certain directory (e.g., R_12.5), check the **log.lammps** for the evolution of a trajectory, and visualize the trajectory with: **vmd mol_sub.xyz trajectory.dcd**
-  - At the end of everything, you can perform averages and integrals by understanding (and using) the script ** get_pot_mean_force **+  - At the end of everything, you can perform averages and integrals by understanding (and using) the script ** get_pot_mean_force **  FROM WITHIN THE DIRECTORY T_300: 
 +<​code>​ 
 +./​get_pot_mean_force 
 +</​code>​ 
 +  - THIS PRODUCES THE POTENTIAL OF MEAN FORCE pot_mean_force for that temperature
   - Repeat the same for other temperatures (e.g.) 10 K and 800 K.   - Repeat the same for other temperatures (e.g.) 10 K and 800 K.
   - Potentials can be visualized by adapting the **gnuplot** script in the exercise_12 directory: pot_mean_force.gnu. Edit and adapt, then:   - Potentials can be visualized by adapting the **gnuplot** script in the exercise_12 directory: pot_mean_force.gnu. Edit and adapt, then:
exercises/2018_ethz_mmm/pmf.txt · Last modified: 2018/05/25 14:42 by dpasserone