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[[Analysis]]


**Brief instruction to obtain order parameter (SCD) by VMD script** \\
Xiaohong Zhuang and Dr. Jeffery B. Klauda \\



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. 


So far, there are three types of VMD scripts that calculate SCD: glycerolphospholipids (gl), sphinoglipids (sl), and cholesterol/sterols (chol). Please select the right type of scd script (folder) based on your lipid. The procedures introduced below are very similar (and simple) for all three types of scripts.


The scripts are in the ZT1 path : **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/scd** \\
or using the zip file: {{ :scd.gz |}}



1. Please copy the script folder(s) for your lipid(s) from the path highlighted above to your directory that has all the dyn files.  


2. In each scd* folder, modify the scd.tcl \\
2a. 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 dcdFile ../dyn$argv.dcd
</code>


2b. 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.


gl lipids have two tails, so we specify both n1 (c3 chain) and n2 (c2 chain); sl lipids have two tails, so we specify both n1 (fa chain) and n2 (s chain); while chol have one chain, so we only specify n2 (chol).


e.g. For scd.tcl file inside gl
<code commend>
set rn "resname DMPE"
set n1 14
set n2 14
</code>


3. In each folder (for each lipid component), modify the scd1.csh.
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 &
$vmd -args 42 > scd42.out &
…
$vmd -args 75 > scd75.out &
</code>


4.  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


<code commend> for (( i=41; i<=75; i++ ))  ! Update the file range to your system </code>


5.  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. The # value will associate to the dyn#.dcd file.


6.  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).


//1-tr3-*-scd-alldyn_avg_title_pos.dat// will be generated which has the final averaged SCD and the standard error.


7. Plot the SCD data that you calculated (SCD vs. Carbon number) by 3_plot_scd.scr, the scd.tif will be generated. But you are free to plot the data by any method that you are comfortable.


**Note**:
1.	For gl lipids, hydrogens attached to Carbon 2 has very different splitting, so the SCD of 2R and 2S are shown separately instead of average in each *.dat that you get after running scd1.csh. The rest values are the average of two/three hydrogens attached to each carbon. For sl or chol, there are not splitting on C2, so there is just one SCD for C2.//
2.	Standard error of average in this SCD calculation is generally so small that can be ignored and it is not necessary to show the error bars in plots.