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--- comp-sa [2021/05/26 10:42] – admin
+++ comp-sa [2023/10/12 11:04] (current) – edit
@@ Line 5: / Line 5: @@
 Instruction to obtain surface area per lipid of **__multicomponent system__** \\
 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 141: / Line 146: @@
 ** Ignore the rest of this wiki for now...Yalun will updated as needed **
 **(Yalun: Following part to be updated)**
 As mentioned above, when submit run-get-areas.scr to run get-area.scr, the combine.csh and avg.csh (also ?dist.csh) are called.