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--- scd [2016/09/20 21:26] – admin
+++ scd [2024/01/25 16:15] (current) – admin
@@ Line 3: / Line 3: @@
 **Brief instruction to obtain order parameter (SCD) by VMD script** \\
-Xiaohong Zhuang, Dr. Jeffery B. Klauda \\
+Xiaohong Zhuang and Dr. Jeffery B. Klauda \\
-Date: 9/18/2015
-This brief instruction is used to order parameter (SCD) by VMD script. The VMD script is run in Deepthought instead of VMD software.
+This brief instruction is used to order parameter (SCD) by VMD script. The VMD script is run on Deepthought2 instead of VMD software on your own computer.
@@ Line 13: / Line 13: @@
-The scripts are in DT1 path: **/lustre/xzhuang/simulation/script_folders/lipids_analyses/scd** \\
+The scripts are in the ZT1 path : **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/scd** \\
-The example output files of gl lipid is in DT1 path:
+or using the zip file: {{ :scd.gz |}}
-**/lustre/xzhuang/simulation/dspc/namd/dyn/gl** \\
@@ Line 21: / Line 21: @@
-. In each scd/* folder, modify the scd.tcl \\
+. In each scd* folder, modify the scd.tcl \\
 a. Update the path for your psf and dcd files (If they are in a different path). No need to change the variable argv in dyn$argv.dcd since it is used in the script later.
 <code commend>
-set psf ../../../step5_assembly.psf
+set psf ../../step5_assembly.psf
 set dcdFile ../dyn$argv.dcd
 </code>
-b. Update the residue name and chain length (which can be found in the topology files in CHARMM toppar folder)
+b. Update the residue name and chain length (which can be found in the topology files in CHARMM toppar folder). If you have several gl lipids then you will need to make separate directories./ for each lipid type.
@@ Line 39: / Line 39: @@
 e.g. For scd.tcl file inside gl
 <code commend>
-set rn "resname PLPC"
+set rn "resname DMPE"
-set n1 16
+set n1 14
-set n2 18
+set n2 14
 </code>
 . In each folder (for each lipid component), modify the scd1.csh.
-Update file range to your system’s equilibrated dyn range (41 to 75 since the system reached equilibrium by 41 dyn, which is obtained by plotting the accumulated average surface area along time).
+Update file range to your system’s equilibrated dyn range (This is a decision made based on the equilibrated time from the surface area/lipid analysis).
 <code commend>
 $vmd -args 41 > scd41.out &
@@ Line 55: / Line 55: @@
-.  In each folder (for each lipid component), modify transp_comb_avg_*.scr, where * represents the type of chains in each type of lipid folder.
+.  In each folder (for each lipid component), modify 2_transp_comb_avg_*.scr, where * represents the type of chains in each type of lipid folder.
 Update the equilibrated file range in the following file to your system
- for (( i=41; i<=75; i++ ))  ! Update the file range to your system
+<code commend> for (( i=41; i<=75; i++ ))  ! Update the file range to your system </code>
-.  Calculate SCD by run the script ''submit.scr ''
+.  Calculate SCD by run the script ''./submit.scr ''
-Note: After run submit.scr, chol-#.dat are obtained for chol, and c2-#.dat, and also c3-#.dat for gl, and fa-#.dat and s-#.dat for sl lipid.
+Note: After run submit.scr, chol-#.dat are obtained for chol, and c2-#.dat, and also c3-#.dat for gl, and fa-#.dat and s-#.dat for sl lipid. The # value will associate to the dyn#.dcd file.
-.  To combine and take the average of 41-75 data.Update the chain lengths in two 3_title*.txt files, and then run the script by command: ''2_transp_comb_avg*.scr''.  (Using the full file name).
+.  To combine and take the average of 41-75 data. Update the text in the two 3_title*.txt files, which should match carbon numbers in your chain typically from 2 to X where X is the last carbon. For the sn-2 chain, 2 is listed twice due to the variation in the two hydrogens on this carbon. Then run the script by command: ''2_transp_comb_avg*.scr''.  (Using the full file name).