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diff --git a/tutorials/README.md b/tutorials/README.md
@@ -1,4 +1,4 @@
 # Tutorials
 
-This folder provides tutorials for setting up and performing simulations of a human nucleus using existing parameters (HFF_100KB), for computing the contact probabilities and optimizing interaction parameters (analysis_code), and for choosing proper initial configurations from the relaxed configuration pool (init_configs).
+This folder provides tutorials for setting up and performing simulations of a human nucleus using existing parameters (HFF_100KB), for computing the contact probabilities (analysis code), for optimizing chr-chr interaction parameters (chr_chr_optimization), for optimizing chr-NL interaction parameters (chr_NL_optimization), and for choosing proper initial configurations from the relaxed configuration pool (init_configs).
 
diff --git a/tutorials/analysis_code/README.md b/tutorials/analysis_code/README.md
@@ -2,22 +2,10 @@
 
 - compute_contact_prob.ipynb: call and computes the contact probabilities (DamID, TSASeq, and chr-chr)
 
-- chr_chr_optimization.ipynb: call and optimizes the chromosome-chromosome interactions (ideal, compt-compt, interchr)
-
-- chr_NL_optimization.ipynb: call and optimizes the chromosome-nuclear landmarks interactions (chr-spe, chr-lam)
-
-- DamID-OE.txt: experimental DamID sequencing data
-
-- TSA-Seq-OE.txt: experimental TSASeq sequencing data
-
 - contact_calculation: execution file compiled from Fortran code "../../openNucleome/utility/chromosome_contact_calculation.f90"
 
 - mol_info: save all the molecular information files necessary for computing contact probabilities
 
-- adam_chr_chr_param: save all the parameters used in the adam optimization for the chromosome-chromosome interactions
-
-- adam_chr_NL_param: save all the parameters used in the adam optimization for the chromosome-nuclear landmarks interactions
-
 - potential: save all the potentials used in the simulations of different iterations
 
 - frame_10.dcd: trajectory file example which contains 10 frames

diff --git a/tutorials/analysis_code/DamID-OE.txt → tutorials/chr_NL_optimization/DamID-OE.txt b/tutorials/analysis_code/DamID-OE.txt → tutorials/chr_NL_optimization/DamID-OE.txt
diff --git a/tutorials/chr_NL_optimization/README.md b/tutorials/chr_NL_optimization/README.md
@@ -0,0 +1,15 @@
+## Analysis code
+
+- chr_NL_optimization.ipynb: call and optimizes the chromosome-nuclear landmarks interactions (chr-spe, chr-lam)
+
+- DamID-OE.txt: experimental DamID sequencing data
+
+- TSA-Seq-OE.txt: experimental TSASeq sequencing data
+
+- mol_info: save all the molecular information files necessary for computing contact probabilities
+
+- adam_chr_NL_param: save all the parameters used in the adam optimization for the chromosome-nuclear landmarks interactions
+
+- potential: save all the potentials used in the chr-NL interactions
+
+- frame_10.dcd: trajectory file example which contains 10 frames
diff --git a/tutorials/analysis_code/TSA-Seq-OE.txt → tutorials/chr_NL_optimization/TSA-Seq-OE.txt b/tutorials/analysis_code/TSA-Seq-OE.txt → tutorials/chr_NL_optimization/TSA-Seq-OE.txt
diff --git a/...sis_code/adam_chr_NL_param/00/mdb_dam.txt → ...mization/adam_chr_NL_param/00/mdb_dam.txt b/...sis_code/adam_chr_NL_param/00/mdb_dam.txt → ...mization/adam_chr_NL_param/00/mdb_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/00/mdb_tsa.txt → ...mization/adam_chr_NL_param/00/mdb_tsa.txt b/...sis_code/adam_chr_NL_param/00/mdb_tsa.txt → ...mization/adam_chr_NL_param/00/mdb_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/00/mdw_dam.txt → ...mization/adam_chr_NL_param/00/mdw_dam.txt b/...sis_code/adam_chr_NL_param/00/mdw_dam.txt → ...mization/adam_chr_NL_param/00/mdw_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/00/mdw_tsa.txt → ...mization/adam_chr_NL_param/00/mdw_tsa.txt b/...sis_code/adam_chr_NL_param/00/mdw_tsa.txt → ...mization/adam_chr_NL_param/00/mdw_tsa.txt
diff --git a/...lysis_code/adam_chr_NL_param/00/t_dam.txt → ...timization/adam_chr_NL_param/00/t_dam.txt b/...lysis_code/adam_chr_NL_param/00/t_dam.txt → ...timization/adam_chr_NL_param/00/t_dam.txt
diff --git a/...lysis_code/adam_chr_NL_param/00/t_tsa.txt → ...timization/adam_chr_NL_param/00/t_tsa.txt b/...lysis_code/adam_chr_NL_param/00/t_tsa.txt → ...timization/adam_chr_NL_param/00/t_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/00/vdb_dam.txt → ...mization/adam_chr_NL_param/00/vdb_dam.txt b/...sis_code/adam_chr_NL_param/00/vdb_dam.txt → ...mization/adam_chr_NL_param/00/vdb_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/00/vdb_tsa.txt → ...mization/adam_chr_NL_param/00/vdb_tsa.txt b/...sis_code/adam_chr_NL_param/00/vdb_tsa.txt → ...mization/adam_chr_NL_param/00/vdb_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/00/vdw_dam.txt → ...mization/adam_chr_NL_param/00/vdw_dam.txt b/...sis_code/adam_chr_NL_param/00/vdw_dam.txt → ...mization/adam_chr_NL_param/00/vdw_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/00/vdw_tsa.txt → ...mization/adam_chr_NL_param/00/vdw_tsa.txt b/...sis_code/adam_chr_NL_param/00/vdw_tsa.txt → ...mization/adam_chr_NL_param/00/vdw_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/01/mdb_dam.txt → ...mization/adam_chr_NL_param/01/mdb_dam.txt b/...sis_code/adam_chr_NL_param/01/mdb_dam.txt → ...mization/adam_chr_NL_param/01/mdb_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/01/mdb_tsa.txt → ...mization/adam_chr_NL_param/01/mdb_tsa.txt b/...sis_code/adam_chr_NL_param/01/mdb_tsa.txt → ...mization/adam_chr_NL_param/01/mdb_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/01/mdw_dam.txt → ...mization/adam_chr_NL_param/01/mdw_dam.txt b/...sis_code/adam_chr_NL_param/01/mdw_dam.txt → ...mization/adam_chr_NL_param/01/mdw_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/01/mdw_tsa.txt → ...mization/adam_chr_NL_param/01/mdw_tsa.txt b/...sis_code/adam_chr_NL_param/01/mdw_tsa.txt → ...mization/adam_chr_NL_param/01/mdw_tsa.txt
diff --git a/...lysis_code/adam_chr_NL_param/01/t_dam.txt → ...timization/adam_chr_NL_param/01/t_dam.txt b/...lysis_code/adam_chr_NL_param/01/t_dam.txt → ...timization/adam_chr_NL_param/01/t_dam.txt
diff --git a/...lysis_code/adam_chr_NL_param/01/t_tsa.txt → ...timization/adam_chr_NL_param/01/t_tsa.txt b/...lysis_code/adam_chr_NL_param/01/t_tsa.txt → ...timization/adam_chr_NL_param/01/t_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/01/vdb_dam.txt → ...mization/adam_chr_NL_param/01/vdb_dam.txt b/...sis_code/adam_chr_NL_param/01/vdb_dam.txt → ...mization/adam_chr_NL_param/01/vdb_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/01/vdb_tsa.txt → ...mization/adam_chr_NL_param/01/vdb_tsa.txt b/...sis_code/adam_chr_NL_param/01/vdb_tsa.txt → ...mization/adam_chr_NL_param/01/vdb_tsa.txt
diff --git a/...sis_code/adam_chr_NL_param/01/vdw_dam.txt → ...mization/adam_chr_NL_param/01/vdw_dam.txt b/...sis_code/adam_chr_NL_param/01/vdw_dam.txt → ...mization/adam_chr_NL_param/01/vdw_dam.txt
diff --git a/...sis_code/adam_chr_NL_param/01/vdw_tsa.txt → ...mization/adam_chr_NL_param/01/vdw_tsa.txt b/...sis_code/adam_chr_NL_param/01/vdw_tsa.txt → ...mization/adam_chr_NL_param/01/vdw_tsa.txt
diff --git a/...analysis_code/adam_chr_NL_param/README.md → ..._optimization/adam_chr_NL_param/README.md b/...analysis_code/adam_chr_NL_param/README.md → ..._optimization/adam_chr_NL_param/README.md
diff --git a/...s/analysis_code/chr_NL_optimization.ipynb → ...NL_optimization/chr_NL_optimization.ipynb b/...s/analysis_code/chr_NL_optimization.ipynb → ...NL_optimization/chr_NL_optimization.ipynb
diff --git a/tutorials/chr_NL_optimization/mol_info/README.md b/tutorials/chr_NL_optimization/mol_info/README.md
@@ -0,0 +1,7 @@
+## Molecular information
+
+- gLengthFile.txt: The difference between each two neighboring values in the file represents the length of the chromosome
+
+- maternalIdxFile.txt: Index of each maternal chromosome
+
+- paternalIdxFile.txt: Index of each paternal chromosome
diff --git a/tutorials/chr_NL_optimization/mol_info/gLengthFile.txt b/tutorials/chr_NL_optimization/mol_info/gLengthFile.txt
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diff --git a/tutorials/chr_NL_optimization/mol_info/maternalIdxFile.txt b/tutorials/chr_NL_optimization/mol_info/maternalIdxFile.txt
@@ -0,0 +1,23 @@
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@@ -0,0 +1,23 @@
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diff --git a/tutorials/chr_NL_optimization/potential/00/README.md b/tutorials/chr_NL_optimization/potential/00/README.md
@@ -0,0 +1,7 @@
+This folder includes all the parameter files needed for the chr-NL interactions
+
+- chr_lam_spec.txt: Chromosome-lamina interaction parameters
+
+- chr_spec_param.txt: Chromosome-speckle interaction parameters
+
+- chr_nuc_param.txt: Chromosome-nucleoli interaction parameters
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