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--- comp-sa [2021/05/26 10:26] – admin
+++ comp-sa [2023/10/12 11:04] (current) – edit
@@ Line 4: / Line 4: @@
 Instruction to obtain surface area per lipid of **__multicomponent system__** \\
-Original Authors: Xiaohong Zhuang and Viviana Monje
+Original Authors: Xiaohong Zhuang and Viviana Monje\\
-Updated Authors: Yalun Yu and Jeffery Klauda
+Updated Authors: Yalun Yu and Jeffery Klauda\\
+Updated rtfpsf folder: Joshua Lucker
-The script is in DT2 path: **/lustre/jbklauda/scripts/area_mult_lipids** \\
+The script is in ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/area_mult_lipids** \\
 or using zip file: {{ area_mult_lipids.gz |}}
@@ Line 92: / Line 93: @@
 As explained in the comments inside test.scr, each values/name following test.csh are the following \\ \\
 <code>
-# *.csh (#chol+3*#lip) (#chol+3*#lip+1) (first dcd count) (last dcd count) (first dcd - first dcd count) (output dir) (CHARMM input) (#lipid types) (image atoms)
+# *.csh (#chol+3*#lip) (#chol+3*#lip+1) (first dcd count) (last dcd count) (first dcd - first dcd count) (output dir) (CHARMM input) (# of dimensions always 2) (image atoms)
 # note "dcd count" refers to number of files being read NOT ACTUAL DCD NAME (next argument)
 # SAME number for "first dcd" in ALL lines
@@ Line 112: / Line 113: @@
 **>> area-a**:  area-a is input file for top leaflet, area-b is for bottom leaflet
-**>> 2**: The lipid types of 2 are used instead of 8. (1-atom represented choline/sterol, and other 3-atoms represented lipids, e.g. glycerol lipids, sphingo lipids). So if you have sterols set this two 2 , if none set to 1.
+**>> 2**: This is the dimension of the tessellation, which is always 2.
-**>> 2970**: "image atoms" = 9*(#chol+3*#lip)=9*(28+3*72)
+**>> 2196**: "image atoms" = 9*(#chol+3*#lip)=9*(28+3*72)
 **8. 2_run-dist-avg.scr**: \\
@@ Line 124: / Line 125: @@
 **9. calc_avg_vertical.py & calc_avg_final.py:** \\
-Update the number of each lipid component per leaflet in the same order as in lipid.dat but remove the sterol flag.
+Update the number of each lipid component per leaflet in the same order as in lipid.dat. If you lack sterol, the first number in the Nlist MUST be zero due to the assumption in calc_avg_vertical.py.
 <code>
 # Update the number of each lipid component per leaflet in the same order as in area-a.inp
 Nlist = [28,12,13,9,5,22,7,4]
 </code>
+**10. rtfpsf.str:** \\
+The file names in the rtfpsf.str file will most likely need to be updated.
 **Run the scripts:** \\
@@ Line 134: / Line 139: @@
-.	Run script by command: 1_test.scr. \\
+.	Run script by command: ''./1_test.scr'' \\
 After run 1_test.scr (which may take about 0.5 ~ 2 hours), tmp and output files for all the dcd file count (1-35 in the example) will be generated. In each dcd count folder, atomic-area.dat will be generated which will have (#data points per dcd) rows and (# of represented atoms) columns. For hypo system here, atomic-area.dat has 1000 rows and 244 columns.
-.	Get the averages and standard errors by command: 2_run-dist-avg.scr. You will see 2_avg_std_final.txt which contains the component area for each lipid type following the order in def_nlip.str.
+.	Get the averages and standard errors by command: ''./2_run-dist-avg.scr''. You will see 2_avg_std_final.txt which contains the component area for each lipid type following the order in def_nlip.str.
+** Ignore the rest of this wiki for now...Yalun will updated as needed **
 **(Yalun: Following part to be updated)**