diff --git a/src/bin/lightdock-rust.rs b/src/bin/lightdock-rust.rs
index 712f43b..202e9b4 100644
--- a/src/bin/lightdock-rust.rs
+++ b/src/bin/lightdock-rust.rs
@@ -129,6 +129,14 @@ fn run() {
     }
 }
 
+fn parse_swarm_id(path: &Path) -> Option<i32> {
+    path.file_name()
+        .and_then(|s| s.to_str())
+        .and_then(|s| s.strip_prefix("initial_positions_"))
+        .and_then(|s| s.strip_suffix(".dat"))
+        .and_then(|s| s.parse::<i32>().ok())
+}
+
 fn simulate(simulation_path: &str, setup: &SetupFile, swarm_filename: &str, steps: u32, method: Method) {
 
     let seed:u64 = match setup.seed {
@@ -141,6 +149,16 @@ fn simulate(simulation_path: &str, setup: &SetupFile, swarm_filename: &str, step
     };
 
     println!("Reading starting positions from {:?}", swarm_filename);
+    let file_path = Path::new(swarm_filename);
+    let swarm_id = parse_swarm_id(file_path).expect("Could not parse swarm from swarm filename");
+    println!("Swarm ID {:?}", swarm_id);
+    let swarm_directory = format!("swarm_{}", swarm_id);
+
+    if !fs::metadata(&swarm_directory).map(|m| m.is_dir()).unwrap_or(false) {
+        panic!("Output directory does not exist for swarm {:?}", swarm_id);
+    }
+
+    println!("Writing to swarm dir {:?}", swarm_directory);
     let positions = parse_input_coordinates(swarm_filename);
 
     // Parse receptor input PDB structure
@@ -206,7 +224,15 @@ fn simulate(simulation_path: &str, setup: &SetupFile, swarm_filename: &str, step
 
     // Glowworm Swarm Optimization algorithm
     println!("Creating GSO with {} glowworms", positions.len());
-    let mut gso = GSO::new(&positions, seed, &scoring, setup.use_anm, setup.anm_rec, setup.anm_lig);
+    let mut gso = GSO::new(
+        &positions,
+        seed,
+        &scoring,
+        setup.use_anm,
+        setup.anm_rec,
+        setup.anm_lig,
+        swarm_directory
+    );
 
     // Simulate for the given steps
     println!("Starting optimization ({} steps)", steps);
diff --git a/src/lib.rs b/src/lib.rs
index ce63a9a..3315664 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -22,15 +22,17 @@ use log::info;
 pub struct GSO<'a> {
     pub swarm: Swarm<'a>,
     pub rng: StdRng,
+    pub output_directory: String
 }
 
 
 impl<'a> GSO<'a> {
     pub fn new(positions: &[Vec<f64>], seed: u64, scoring: &'a Box<dyn Score>, use_anm: bool,
-        rec_num_anm: usize, lig_num_anm: usize) -> Self {
+        rec_num_anm: usize, lig_num_anm: usize, output_directory: String) -> Self {
         let mut gso = GSO {
             swarm: Swarm::new(),
             rng: SeedableRng::seed_from_u64(seed),
+            output_directory
         };
         gso.swarm.add_glowworms(positions, scoring, use_anm, rec_num_anm, lig_num_anm);
         gso
@@ -42,7 +44,7 @@ impl<'a> GSO<'a> {
             self.swarm.update_luciferin();
             self.swarm.movement_phase(&mut self.rng);
             if step % 10 == 0 || step == 1 {
-                match self.swarm.save(step) {
+                match self.swarm.save(step, &self.output_directory) {
                     Ok(ok) => ok,
                     Err(why) => panic!("Error saving GSO output: {:?}", why),
                 }
diff --git a/src/swarm.rs b/src/swarm.rs
index cd45080..2b13846 100644
--- a/src/swarm.rs
+++ b/src/swarm.rs
@@ -112,8 +112,8 @@ impl<'a> Swarm<'a> {
         }
     }
 
-    pub fn save(&mut self, step: u32) -> Result<(), Error> {
-        let path = format!("gso_{:?}.out", step);
+    pub fn save(&mut self, step: u32, output_directory: &str) -> Result<(), Error> {
+        let path = format!("{}/gso_{:?}.out", output_directory, step);
         let mut output = File::create(path)?;
         writeln!(output, "#Coordinates  RecID  LigID  Luciferin  Neighbor's number  Vision Range  Scoring")?;
         for glowworm in self.glowworms.iter() {