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exercises:2018_ethz_mmm:pmf [2018/05/25 10:55] – dpasseroneexercises: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:
-<code> cp run* *pot c1.topo l1_temp.inp T_300 get_pot_mean_force ; cd T_300 </code> +<code> cp run* *pot c1.topo md_temp.inp get_pot_mean_force T_300  ; cd T_300 </code> 
   * 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_ 100 
-fix temp2 substrate nvt temp 300 300 100 +fix temp2 substrate nvt temp _TEMP_ _TEMP_ 100 
-velocity                        all create 300 293288+velocity                        all create _TEMP_ 293288
 fix PMF molecule recenter NULL _Y_ NULL fix PMF molecule recenter NULL _Y_ NULL
 compute temp_molecule molecule temp compute temp_molecule molecule temp
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 thermo_modify flush yes thermo_modify flush yes
 thermo 50 thermo 50
-dump xyz all xyz 100000 mol_sub.xyz+dump xyz all xyz 100000000 mol_sub.xyz
 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 500000 TCB_PMF.restart+restart _NSTEPS_ TCB_PMF.restart
 run _NSTEPS_              run _NSTEPS_             
 </code> </code>
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 <note important> <note important>
-  - Edit the input file to run 50 picoseconds. These are not a lot, but the simulation will last a few minutes per distance.+  - 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 making the exercise feasible on 16 cores.
   - Now run the chain of simulations   - Now run the chain of simulations
 <code> qsub run_distance_loop </code> <code> qsub run_distance_loop </code>
   - Directories R_<distance> will be created (check with ** ls -ltr ** )   - Directories R_<distance> will be created (check with ** ls -ltr ** )
-  - You can enter a certain directory (e.g., R_12.5) and visualize it 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: 
 +<code> 
 +./get_pot_mean_force 
 +</code> 
 +  - 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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 </code> </code>
 </note> </note>
 +<note important> 
 +Check the already finished runs in REF_300:  
 +<code> 
 +cd REF_300 
 +cp ../get_pot_mean_force . 
 +./get_pot_mean_force 
 +gnuplot 
 +gnuplot > plot "pot_mean_force" w lp  
 +</code> 
 +</note>
  
 <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?
 </note> </note>
  
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