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--- exercises:2018_ethz_mmm:pmf [2018/05/25 11:13] – dpasserone
+++ exercises:2018_ethz_mmm:pmf [2018/05/25 14:22] – dpasserone
@@ Line 95: / Line 95: @@
 <note important>
-  - 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 making the exercise feasible on 16 cores.
+  - 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: