Add the pair_modify shift command and visualisation tips

tut0_lj_fluid/init.sh

@@ -180,6 +180,11 @@ run ${run_init_time}
 # If rc > 2^(1/6), then there is a region where the potential is attractive
 pair_style lj/cut ${rc_0}
 
+# Make sure the LJ potential is shifted by the energy value at the cutoff.
+# This only changes the pairwise energy values output by LAMMPS but has no
+# effect on the actual dynamics
+pair_modify shift yes
+
 # Set the params for the pairwise interactions between individual atom types
 # Key params: atom_type_1 atom_type_2 epsilon sigma rc
 # Try changing epsilon and rc (cutoff) and see how that affects the dynamics!

tut1_polymer/init.sh

@@ -221,6 +221,7 @@ angle_coeff 1 ${l_p}
 
 # Switch from soft to the purely repulsive LJ (or WCA) potential
 pair_style lj/cut ${rc_0}
+pair_modify shift yes
 pair_coeff * * 1.0 ${sigma} ${rc_0}
 
 run ${run_init_time_2}

tut2_dna_protein/init.sh

@@ -213,6 +213,7 @@ angle_coeff 1 ${l_p}
 
 # Switch from soft to the purely repulsive LJ (or WCA) potential
 pair_style lj/cut ${rc_0}
+pair_modify shift yes
 pair_coeff * * 1.0 ${sigma} ${rc_0}
 
 run ${run_init_time_2}

vmd_visualisation_tips.txt

+Note that because LAMMPS does not output the bead positions in order (i.e., by
+the bead index) while VMD thinks that is the case, beads are linked together
+wrongly in the visualisation. We can fix this by typing the following set of
+commands in the terminal after loading the molecule:
+
+      topo clearbonds
+      set N {nbeads}
+      for {set i 0} {$i < [expr $N-1]} {incr i} {
+      	  set j [expr $i+1]
+	  topo addbond $i $j
+      }
+
+[You will need to replace the variable nbeads with the actual number of beads
+in the polymer]
+