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--- exercises:2018_ethz_mmm:pmf [2018/05/25 10:39] – dpasserone
+++ exercises:2018_ethz_mmm:pmf [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 44: / Line 44: @@
 <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 ** run* *pot c1.topo **
+  * Create a directory T_300 and copy into it the following files and cd into the directory:
-</note>
+<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.
+  * How many steps will you run per each distance? This will be decided by editing the input file.
+</note>
+<code - md_temp.inp >
+# PMF Input script template
+# (1) Initialisation
+units real
+atom_style full
+boundary p p p
+pair_style hybrid/overlay lj/charmm/coul/long 10.0 12.0 buck/coul/long 12.0 morse 10.0
+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                        all create _TEMP_ 293288
+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_
+</code>
+<note important>
+  - 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
+<code> qsub run_distance_loop </code>
+  - Directories R_<distance> will be created (check with ** ls -ltr ** )
+  - 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:
+<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.
+  - Potentials can be visualized by adapting the **gnuplot** script in the exercise_12 directory: pot_mean_force.gnu. Edit and adapt, then:
+<code> gnuplot
+gnuplot> load "pot_mean_force.gnu"
+</code>
+</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>
+  - 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? Why?
+  - Can you say something about the entropy contributions?
+</note>