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Brief instruction to obtain order parameter (SCD) by VMD script
Xiaohong Zhuang, 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.
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 DT1 path: /lustre/xzhuang/simulation/script_folders/lipids_analyses/scd
The example output files of gl lipid is in DT1 path:
/lustre/xzhuang/simulation/dspc/namd/dyn/gl
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$argv.dcd since it is used in the script later.
set psf ../../../step5_assembly.psf set dcdFile ../dyn$argv.dcd
2b. Update the residue name and chain length (which can be found in the topology files in CHARMM toppar folder)
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
set rn "resname PLPC" set n1 16 set n2 18
3. 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).
$vmd -args 41 > scd41.out & $vmd -args 42 > scd42.out & … $vmd -args 75 > scd75.out &
4. In each folder (for each lipid component), modify 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 1) ! Update the file range to your system
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.
6. 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).
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.