exercises:2018_ethz_mmm:pmf
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| Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
| 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_< | - Directories R_< | ||
| - 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: |
| + | < | ||
| + | ./ | ||
| + | </ | ||
| + | - 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: 2020/08/21 10:15 by 127.0.0.1