Differences

This shows you the differences between two versions of the page.

--- lipid_clustering [2017/02/10 15:10] – admin
+++ lipid_clustering [2022/11/07 08:46] (current) – admin
@@ Line 7: / Line 7: @@
 This instruction is explain the procedure to perform the clustering analysis of multiple lipid bilayers.
-Script in DT1: /lustre/xzhuang/simulation/script_folders/lipids_analyses/cluster_mult_lip\\
+Download Script: {{ ::clus-s.tar.gz |}}\\
-Example in DT1: /lustre/xzhuang/simulation/script_folders/lipids_analyses/cluster_mult_lip_eg\\
-Example in DT2: /lustre/xzhuang/soybean/1_analyses/cluster_all/root-1
-Download Script: {{ ::clus-s.tar.gz |}}
 Download Example: {{ :clus-e.tar.gz |}}
 Copy the script folder provided in the path above to your path.
+If on ZT1, please use the files in the following directory: /afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/cluster_mult_lip/
 =====Cluster Prep=====
@@ Line 22: / Line 20: @@
 .1 Update the path of psf and crd files in **rtfpsf.str**
-.2 Update the path of **step5_assembly.str**, **crystal_image.str**, and dcd files in **coord-a.inp** and **coord-b.inp**
+.2 Update the path of **step5_assembly.str**, **crystal_image.str**, **dcd files** and **number of frames per dcd** in **coord-a.inp** and **coord-b.inp**
 .3 Update the lipid names and head group names, and number of types of three groups of lipids in the **def_nlip_a.str** and **def_nlip_b.str**.
@@ Line 75: / Line 73: @@
 Multiple tests may be required to obtain reasonable Dcut. The Dcut is selected so that the majority of Nlf in **tot-*.txt** is less than 75% of total lipid number per leaflet, and the majority of Nlc in **num-*.txt** is greater or equal to 4. You may discuss on this with Dr.Klauda.
-.3 Submit the job by ''2b_submit_sbatch.scr''. (May update the walltime requirement in **2b-run-dbscan.csh** when necessary.)
+.3 Submit the job by ''2b_submit_sbatch.scr''. (May update the walltime requirement in **2b-run-dbscan.csh** when necessary. Also update Nf and Nlip, Nf should be 1/10 the actual number of frames to save time)
 After the run, the **dbscan-*.txt**, **tot-*.txt**, and **num-*.txt** and will be obtained.
@@ Line 91: / Line 89: @@
 .5 Then, obtain the top and bottom average by command: ''2h-tb-avg.scr''
-The final results are shown in tb-avg folder. In the **final-Nlc-avg.txt**, with four rows are averaged number of lipid per cluster (Nc), the fraction of lipid per cluster (Rc) and overall lipid composition ratio (Rn), and the difference between the cluster fraction (ratio) and overall composition ratio (Rc-Rn).
+The final results are shown in tb-avg folder. In the **final-Nlc-avg.txt**, with five rows are averaged number of lipid per cluster (Nc), the fraction of lipid per cluster (Rc) and overall lipid composition ratio (Rn), the difference between the cluster fraction (ratio) and overall composition ratio (Rc-Rn), and lastly, the relative difference between the cluster fraction ratio and overall composition ratio (Rc-Rn)/Rn.
 =====Visualize=====