Corrected paths in gmx distance call, and return the right part of the output
@@ -19,7 +19,10 @@ cd $WEST_SIM_ROOT
DIST=$(mktemp)
# Calculate the distance between Na+ and Cl-
-$GMX distance -f $WEST_STRUCT_DATA_REF -s $WEST_STRUCT_DATA_REF -oall $DIST \
+$GMX distance \
+ -f $WEST_STRUCT_DATA_REF/seg.trr \
+ -s $WEST_STRUCT_DATA_REF/seg.gro \
+ -oall $DIST \
-select 1
# Return the distance between Na+ and Cl- WESTPA.
@@ -37,4 +40,3 @@ rm $DIST.xvg
if [ -n "$SEG_DEBUG" ] ; then
head -v $WEST_PCOORD_RETURN
fi
-
