Symlink files from ./prep directory when initializing simulation
@@ -22,6 +22,20 @@ pkill -9 -f w_run
rm -rf traj_segs seg_logs istates west.h5
mkdir seg_logs traj_segs istates
+# Symlink the results of the equilibration to the bstates directory
+rm -rf bstates/unbound
+mkdir bstates/unbound
+cd bstates/unbound || exit 1
+ln -s ../../prep/5_eq2/5_eq2.gro seg.gro
+ln -s ../../prep/5_eq2/5_eq2.trr seg.trr
+ln -s ../../prep/5_eq2/5_eq2.edr seg.edr
+cd ../../
+
+# Also symlink the topology file
+cd gromacs_config || exit 1
+ln -s ../prep/1_pdb2gmx/topol.top nacl.top
+cd ../
+
# Define the arguments for the basis states (used for generating initial
# states; in this case we only have one), and target states (used for
# knowing when to recycle trajectories). In this example, we recycle
