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--- exercises:2018_ethz_mmm:pmf [2018/05/25 11:09] – dpasserone
+++ exercises:2018_ethz_mmm:pmf [2018/05/25 14:42] – dpasserone
@@ 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 and cd into the directory:
 <code> cp run* *pot c1.topo md_temp.inp get_pot_mean_force T_300  ; cd T_300 </code>
@@ Line 77: / Line 77: @@
 timestep 1.0
 # (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
 compute temp_molecule molecule temp
@@ Line 86: / Line 86: @@
 thermo_modify flush yes
 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 coord all dcd 5000 trajectory.dcd
-restart 500000 TCB_PMF.restart
+restart _NSTEPS_ TCB_PMF.restart
 run _NSTEPS_
 </code>
@@ Line 95: / Line 95: @@
 <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
 <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 **
+  - 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:
@@ Line 107: / Line 113: @@
 </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>