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--- exercises:2018_ethz_mmm:pmf [2018/05/25 11:09] – dpasserone
+++ exercises:2018_ethz_mmm:pmf [2018/05/25 11:13] – 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.  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>