diff --git a/examples/HIVdynamics_aMCMC/README.txt b/examples/HIVdynamics_aMCMC/README.txt
index daddd6ff..6b5e2f67 100644
--- a/examples/HIVdynamics_aMCMC/README.txt
+++ b/examples/HIVdynamics_aMCMC/README.txt
@@ -1,5 +1,5 @@
 A model parameterization of the two-phase exponential decay model for viral dynamics under therapy 
-generated from published models (1,2).
+generated from the following publications (1,2).
 
 The first run was done for 100000 iterations to find a suitable covariance matrix and to find convergence. 
 The Warm start following was ran for 200000 total iterations and was able to properly sample the posterior distribution. 
diff --git a/examples/HIVdynamics_aMCMC/pt303.bngl b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303.bngl
rename to examples/HIVdynamics_aMCMC/pt303/pt303.bngl
diff --git a/examples/HIVdynamics_aMCMC/pt303.conf b/examples/HIVdynamics_aMCMC/pt303/pt303.conf
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303.conf
rename to examples/HIVdynamics_aMCMC/pt303/pt303.conf
diff --git a/examples/HIVdynamics_aMCMC/pt303.exp b/examples/HIVdynamics_aMCMC/pt303/pt303.exp
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303.exp
rename to examples/HIVdynamics_aMCMC/pt303/pt303.exp
diff --git a/examples/HIVdynamics_aMCMC/pt303.sh b/examples/HIVdynamics_aMCMC/pt303/pt303.sh
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303.sh
rename to examples/HIVdynamics_aMCMC/pt303/pt303.sh
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt
rename to examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt
rename to examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt
rename to examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt
diff --git a/examples/HIVdynamics_aMCMC/pt403.bngl b/examples/HIVdynamics_aMCMC/pt403/pt403.bngl
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403.bngl
rename to examples/HIVdynamics_aMCMC/pt403/pt403.bngl
diff --git a/examples/HIVdynamics_aMCMC/pt403.conf b/examples/HIVdynamics_aMCMC/pt403/pt403.conf
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rename from examples/HIVdynamics_aMCMC/pt403.conf
rename to examples/HIVdynamics_aMCMC/pt403/pt403.conf
diff --git a/examples/HIVdynamics_aMCMC/pt403.exp b/examples/HIVdynamics_aMCMC/pt403/pt403.exp
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403.exp
rename to examples/HIVdynamics_aMCMC/pt403/pt403.exp
diff --git a/examples/HIVdynamics_aMCMC/pt403.sh b/examples/HIVdynamics_aMCMC/pt403/pt403.sh
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403.sh
rename to examples/HIVdynamics_aMCMC/pt403/pt403.sh
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt
rename to examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt
rename to examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt
rename to examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt
diff --git a/examples/HIVdynamics_aMCMC/pt409.bngl b/examples/HIVdynamics_aMCMC/pt409/pt409.bngl
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rename from examples/HIVdynamics_aMCMC/pt409.bngl
rename to examples/HIVdynamics_aMCMC/pt409/pt409.bngl
diff --git a/examples/HIVdynamics_aMCMC/pt409.conf b/examples/HIVdynamics_aMCMC/pt409/pt409.conf
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409.conf
rename to examples/HIVdynamics_aMCMC/pt409/pt409.conf
diff --git a/examples/HIVdynamics_aMCMC/pt409.exp b/examples/HIVdynamics_aMCMC/pt409/pt409.exp
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409.exp
rename to examples/HIVdynamics_aMCMC/pt409/pt409.exp
diff --git a/examples/HIVdynamics_aMCMC/pt409.sh b/examples/HIVdynamics_aMCMC/pt409/pt409.sh
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409.sh
rename to examples/HIVdynamics_aMCMC/pt409/pt409.sh
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt
rename to examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt
rename to examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt
similarity index 100%
rename from examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt
rename to examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt