exercises:2018_ethz_mmm:pmf
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
exercises:2018_ethz_mmm:pmf [2018/05/25 10:19] – created dpasserone | exercises:2018_ethz_mmm:pmf [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 43: | Line 43: | ||
Then we will use integration of the average force between the molecule and the substrate, along the adsorption path, to extract the free energy difference between two configurations: | Then we will use integration of the average force between the molecule and the substrate, along the adsorption path, to extract the free energy difference between two configurations: | ||
+ | <note important> | ||
+ | * 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: | ||
+ | < | ||
+ | * 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. | ||
+ | </ | ||
+ | <code - md_temp.inp > | ||
+ | # PMF Input script template | ||
+ | # (1) Initialisation | ||
+ | units real | ||
+ | atom_style full | ||
+ | boundary p p p | ||
+ | pair_style hybrid/ | ||
+ | bond_style harmonic | ||
+ | angle_style harmonic | ||
+ | dihedral_style charmm | ||
+ | kspace_style pppm 0.0001 | ||
+ | # (2) Define atoms | ||
+ | read_data c1.topo | ||
+ | group molecule molecule 1 | ||
+ | group substrate molecule 2 | ||
+ | group bottom molecule 3 | ||
+ | # (3) Settings | ||
+ | # freeze bottom layer of substrate to prevent it from drifting | ||
+ | fix 2 bottom setforce 0 0 0 | ||
+ | include new_defpot.pot | ||
+ | include best_all.pot | ||
+ | neighbor 2.0 bin | ||
+ | neigh_modify delay 0 | ||
+ | timestep 1.0 | ||
+ | # (4) NVT Dynamics | ||
+ | fix temp1 molecule nvt temp _TEMP_ _TEMP_ 100 | ||
+ | fix temp2 substrate nvt temp _TEMP_ _TEMP_ 100 | ||
+ | velocity | ||
+ | fix PMF molecule recenter NULL _Y_ NULL | ||
+ | compute temp_molecule molecule temp | ||
+ | compute yforce molecule group/group substrate kspace yes | ||
+ | thermo_style custom time c_yforce[2] etotal pe c_temp_molecule temp ke evdwl press enthalpy | ||
+ | thermo_modify flush yes | ||
+ | thermo 50 | ||
+ | dump xyz all xyz 100000000 mol_sub.xyz | ||
+ | dump_modify xyz element C C H C N K Cl | ||
+ | dump coord all dcd 5000 trajectory.dcd | ||
+ | restart _NSTEPS_ TCB_PMF.restart | ||
+ | run _NSTEPS_ | ||
+ | </ | ||
+ | |||
+ | |||
+ | <note important> | ||
+ | - 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 | ||
+ | < | ||
+ | - 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** | ||
+ | - 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. | ||
+ | - Potentials can be visualized by adapting the **gnuplot** script in the exercise_12 directory: pot_mean_force.gnu. Edit and adapt, then: | ||
+ | < | ||
+ | gnuplot> load " | ||
+ | </ | ||
+ | </ | ||
+ | <note important> | ||
+ | Check the already finished runs in REF_300: | ||
+ | < | ||
+ | cd REF_300 | ||
+ | cp ../ | ||
+ | ./ | ||
+ | gnuplot | ||
+ | gnuplot > plot " | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | <note warning> | ||
+ | - Report adsorption (free) energy and equilibrium distance for the three temperatures. What do you note? | ||
+ | - 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? | ||
+ | - Can you say something about the entropy contributions? | ||
+ | </ | ||
exercises/2018_ethz_mmm/pmf.1527243542.txt.gz · Last modified: 2020/08/21 10:15 (external edit)