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--- pairwise_2d-rdf_and_clustering [2022/10/14 17:20] – edit
+++ pairwise_2d-rdf_and_clustering [2022/10/23 21:33] (current) – [Pairwise 2D-RDF and Clustering Analysis] edit
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 * use lower case for head group name but upper case for atom name.
-b. In **run_cluster.py**, the pair specific Dcut can be implemented by the **clfix** argument when creating a ClusterLip instance (see the code and you will know what I mean). The minimum number of lipids in a cluster can be modified using the **min_lipids** argument. Other changes should follow the instructions in the code.
+b. In **run_cluster.py**, the pair specific Dcut can be implemented by the **clfix** argument when creating a ClusterLip instance (see the code and you will know what I mean). The minimum number of lipids in a cluster can be modified using the **min_lipids** argument.
+c. Include ALL lipids in your system.
+d. Other changes should follow the instructions in the code.
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 * Could also use //"else:"// command to minimize repetitive line entry for colors of lipids not of our interest
-d. Usually it takes about 10 seconds to generate two cluster pictures (upper&lower leaflets) for one frame, so that I won't use slurm. So, just type python visualize.py and wait for a while (remember to activate the conda env you created). However, if you want to create pictures for more than 10 frames, please consider using slurm. Again, the instructions are within the code.
+d. You can define what's included in the cluster plot by editing the //top_res_info// and //bot_res_info// in visualize.py. (Note: the code structure is identical to that in //run_cluster.py//, but you do not have to include all lipids in the system and just the lipids of interest.)
+e. Usually it takes about 10 seconds to generate two cluster pictures (upper&lower leaflets) for one frame, so that I won't use slurm. So, just type python visualize.py and wait for a while (remember to activate the conda env you created). However, if you want to create pictures for more than 10 frames, please consider using slurm. Again, the instructions are within the code.