exercises:2018_ethz_mmm:pmf
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
exercises:2018_ethz_mmm:pmf [2018/05/25 11:09] – dpasserone | exercises:2018_ethz_mmm:pmf [2018/05/25 14:19] – dpasserone | ||
---|---|---|---|
Line 44: | Line 44: | ||
<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: | ||
< | < | ||
Line 77: | Line 77: | ||
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_ | ||
</ | </ | ||
Line 95: | Line 95: | ||
<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. 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), 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