scd
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scd [2016/11/16 15:40] – admin | scd [2024/01/25 16:15] (current) – admin | ||
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- | This brief instruction is used to order parameter (SCD) by VMD script. The VMD script is run in Deepthought | + | This brief instruction is used to order parameter (SCD) by VMD script. The VMD script is run on Deepthought2 |
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- | 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/ |
- | The example output files of gl lipid is in DT1 path: | + | or using the zip file: {{ :scd.gz |}} |
- | **/ | + | |
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- | 2. In each scd/* folder, modify the scd.tcl \\ | + | 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$argv.dcd since it is used in the script later. | 2a. Update the path for your psf and dcd files (If they are in a different path). No need to change the variable argv in dyn$argv.dcd since it is used in the script later. | ||
<code commend> | <code commend> | ||
- | set psf ../../ | + | set psf ../ |
set dcdFile ../ | set dcdFile ../ | ||
</ | </ | ||
- | 2b. Update the residue name and chain length (which can be found in the topology files in CHARMM toppar folder) | + | 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./ |
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e.g. For scd.tcl file inside gl | e.g. For scd.tcl file inside gl | ||
<code commend> | <code commend> | ||
- | set rn " | + | set rn " |
- | set n1 16 | + | set n1 14 |
- | set n2 18 | + | set n2 14 |
</ | </ | ||
3. In each folder (for each lipid component), modify the scd1.csh. | 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 | + | 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> | <code commend> | ||
$vmd -args 41 > scd41.out & | $vmd -args 41 > scd41.out & | ||
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- | 4. In each folder (for each lipid component), modify | + | 4. In each folder (for each lipid component), modify |
Update the equilibrated file range in the following file to your system | Update the equilibrated file range in the following file to your system | ||
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- | 5. Calculate SCD by run the script '' | + | 5. Calculate SCD by run the script '' |
- | 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. |
- | 6. To combine and take the average of 41-75 data.Update the chain lengths | + | 6. To combine and take the average of 41-75 data. Update the text in the two 3_title*.txt files, |
scd.1479328808.txt.gz · Last modified: 2016/11/16 15:40 (external edit)