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 [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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<note important> | <note important> | ||
- | - Edit the input file to run 50 picoseconds, | + | - Edit the input file to run 50 picoseconds, |
+ | - **REPLACE _NSTEPS_ WITH THE NUMBER OF STEPS AND _TEMP_ WITH THE DESIRED TEMPERATURE IN THE md_temp.inp FILE** | ||
+ | - The length of the simulation is small to get converged averages, but the run will thus last a few minutes per distance making the exercise feasible on 16 cores. | ||
- Now run the chain of simulations | - Now run the chain of simulations | ||
< | < | ||
- 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: | ||
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</ | </ | ||
</ | </ | ||
+ | <note important> | ||
+ | Check the already finished runs in REF_300: | ||
+ | < | ||
+ | cd REF_300 | ||
+ | cp ../ | ||
+ | ./ | ||
+ | gnuplot | ||
+ | gnuplot > plot " | ||
+ | </ | ||
+ | </ | ||
<note warning> | <note warning> |
exercises/2018_ethz_mmm/pmf.1527246815.txt.gz · Last modified: 2020/08/21 10:15 (external edit)