exercises:2018_ethz_mmm:pmf
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exercises:2018_ethz_mmm:pmf [2018/05/25 10:55] – 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> | ||
- | * After you copied the exercise_12 directory and entered it, look at the l1.xyz file (by editing or vmd) and understand the geometry of the system: which range of distances should you consider for MD runs? | + | * After you copied the exercise_12 directory and entered it, look at the mol_sub.xyz file (by editing or vmd) and understand the geometry of the system: which range of distances should you consider for MD runs? |
* Create a directory T_300 and copy into it the following files and cd into the directory: | * Create a directory T_300 and copy into it the following files and cd into the directory: | ||
- | < | + | < |
* At this point edit the **run_distance_loop** script and insert the list of distances you want to simulate. | * At this point edit the **run_distance_loop** script and insert the list of distances you want to simulate. | ||
* How many steps will you run per each distance? This will be decided by editing the input file. | * How many steps will you run per each distance? This will be decided by editing the input file. | ||
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timestep 1.0 | timestep 1.0 | ||
# (4) NVT Dynamics | # (4) NVT Dynamics | ||
- | fix temp1 molecule nvt temp 300 300 100 | + | fix temp1 molecule nvt temp _TEMP_ _TEMP_ |
- | fix temp2 substrate nvt temp 300 300 100 | + | fix temp2 substrate nvt temp _TEMP_ _TEMP_ |
- | velocity | + | velocity |
fix PMF molecule recenter NULL _Y_ NULL | fix PMF molecule recenter NULL _Y_ NULL | ||
compute temp_molecule molecule temp | compute temp_molecule molecule temp | ||
Line 86: | Line 86: | ||
thermo_modify flush yes | thermo_modify flush yes | ||
thermo 50 | thermo 50 | ||
- | dump xyz all xyz 100000 | + | dump xyz all xyz 100000000 |
dump_modify xyz element C C H C N K Cl | dump_modify xyz element C C H C N K Cl | ||
dump coord all dcd 5000 trajectory.dcd | dump coord all dcd 5000 trajectory.dcd | ||
- | restart | + | restart |
run _NSTEPS_ | run _NSTEPS_ | ||
</ | </ | ||
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<note important> | <note important> | ||
- | - Edit the input file to run 50 picoseconds. | + | - Edit the input file to run 50 picoseconds, to write the restart at the end, to thermalize at the wished temperature |
+ | - **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 | ||
- 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) and visualize | + | - You can enter a certain directory (e.g., R_12.5), check the **log.lammps** for the evolution of a trajectory, |
- | - 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> | ||
- Report adsorption (free) energy and equilibrium distance for the three temperatures. What do you note? | - Report adsorption (free) energy and equilibrium distance for the three temperatures. What do you note? | ||
- Compare the results with the paper | - Compare the results with the paper | ||
- | - Compare your results with results extracted from REF_10, REF_300, REF_800 that contain longer equilibrations and averaging (about 0.5-1 ns each distance). Where do you get more differences? | + | - Compare your results with results extracted from REF_10, REF_300, REF_800 that contain longer equilibrations and averaging (about 0.5-1 ns each distance). Where do you get more differences? Why? |
+ | - Can you say something about the entropy contributions? | ||
</ | </ | ||
exercises/2018_ethz_mmm/pmf.1527245722.txt.gz · Last modified: 2020/08/21 10:15 (external edit)