comp-sa
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
comp-sa [2020/08/04 10:58] – edit | comp-sa [2023/10/12 11:04] (current) – edit | ||
---|---|---|---|
Line 3: | Line 3: | ||
==== Multi-lipid SA Average ==== | ==== Multi-lipid SA Average ==== | ||
- | Brief instruction | + | Instruction |
- | Authors: Xiaohong Zhuang and Viviana Monje | + | Original |
+ | Updated Authors: Yalun Yu and Jeffery Klauda\\ | ||
+ | Updated rtfpsf folder: Joshua Lucker | ||
- | Original instruction (Viviana Monje): | + | The script is in ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/ |
- | + | ||
- | **NEED** (without any update)\\ | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | '' | + | |
- | + | ||
- | **UPDATE/MODIFY** | + | |
- | ^Code ^Do ^ | + | |
- | |area.c | define NTOT 244 /* //number of atoms being looked per leaflet// */ \\ Re-compile the file using: '' | + | |
- | |area-a.inp & area-b.inp | EndOfFile (EOF) – update argument values for //area.csh// line: \\ '' | + | |
- | |rtfpsf.str | Check file names | | + | |
- | |lipid.dat | 1 (#sterols) (#lipids) \\PER LEAFLET | | + | |
- | |get-areas.scr (no longer needed) | For lipids: //file.csh (# files) (first file)// \\ For average: //file.csh (sterol fraction) (lipid fraction) out-file// (to be copy to a common directory)| | + | |
- | |top & bot (only needed for comp area distribution) | Check values in last line – frames per DCD (usually 500 500 OR 1000 1000 – check dyn-2.inp) \\ \\ // # lipids in the system// \\ // | + | |
- | |avg.csh (no longer needed) | UPDATE path of common directory to store final files if needed \\ (second-to-last line, just update path) | | + | |
- | |1_test.scr| see Xiao's instruction| | + | |
- | |2_run-dist-avg.scr| see Xiao's instruction| | + | |
- | |calc_avg_vertical.py| see Xiao's instruction| | + | |
- | |calc_avg_final.py| see Xiao's instruction| | + | |
- | + | ||
- | (**This no longer true after the most recent updates, see Xiao's instruction instead.**) MAKE SURE the common directory to store all final (average) files exists AND has system.scr (update name of files that you want to combine/ | + | |
- | RUN “test.scr” - Go INTO “tmp” directory and RUN “get-areas.scr” | + | |
- | RUN areas.dat in the common dir. (SYSTEM – CHOLarea – CHOLerror – LIParea – LIPerror – SAsystem) | + | |
- | + | ||
- | + | ||
- | \\ | + | |
- | + | ||
- | **Additional Notes/ | + | |
- | \\ | + | |
- | + | ||
- | The script is in DT2 path: **/lustre/ | + | |
or using zip file: {{ area_mult_lipids.gz |}} | or using zip file: {{ area_mult_lipids.gz |}} | ||
- | |||
- | Besides files mentioned above, you will see some additional files. But you don’t need to edit these files unless you have more than 5 types of sterols, or 10 types of glycerophosphate lipids, or 10 types of sphingo lipids, (or cardiolinpin which will be added later). They are: | ||
- | |||
- | Image-top.str, | ||
**How to Edit and Run the Scripts:** | **How to Edit and Run the Scripts:** | ||
Line 54: | Line 16: | ||
**1. def_nlip.str: | **1. def_nlip.str: | ||
- | (i) Update the resname of lipids. The variable names used for resnames with prefix rnc for sterol, rng for glycerol lipids, rns for sphingo lipids. | + | (i) Update the resname of lipids. The variable names used for resnames with prefix rnc for sterol, rng for glycerol lipids, rns for sphingo lipids. If you do not have a lipid of a specific class then remove the rn* line. You should only have a list of lipids that exists for your system. |
'' | '' | ||
Line 71: | Line 33: | ||
- | **2. area.csh**: Update the path of qhull-2003.1 | + | **2. area.csh**: Update the path of qhull-2003.1, if needed. Current setup is relative to the areas directory. |
**3. area.c**: | **3. area.c**: | ||
Line 77: | Line 39: | ||
# (NTOT in area.c (# of atoms) is not NTOT in area*.inp (# of frames of each dcd file)) | # (NTOT in area.c (# of atoms) is not NTOT in area*.inp (# of frames of each dcd file)) | ||
- | (# | ||
- | Eg. For hypocotyl system, with 28 sterols and 72 lipids, (per leaflet), NTOT=28+3*72=244 | ||
- | \\ | ||
- | **compile this C code with gcc: "gcc area.c -o area.exe" | ||
- | **4. area-a.inp & area-b.inp**: | + | (NTOT=# |
- | Update file paths; Update | + | |
+ | For example with the hypocotyl plant membrane | ||
\\ | \\ | ||
+ | |||
+ | **Must compile this C code with gcc**: '' | ||
+ | |||
+ | **4. area-a.inp & area-b.inp**: | ||
+ | |||
+ | Update file paths: in rtfpsf.str, for step5_assembly.str, | ||
+ | TOPPAR Files: It is easiest if you copy the toppar.str file and its associated toppar directory from the CHARMM-GUI/ | ||
+ | Update the system size a,b,c based on dyn.xsc (the 2nd-4th non-zero values) in your dyn directory \\ | ||
+ | Update the number of frames in each DCD: '' | ||
+ | Update atom numbers: \\ | ||
+ | < | ||
+ | ! *.csh (directory) (#chol + 3*#lipids + 1) (#chol + 3*#lipids) ! per leaflet | ||
+ | system " | ||
+ | </ | ||
+ | |||
**5. lipid.dat**: | **5. lipid.dat**: | ||
Line 96: | Line 70: | ||
**6. top/bot (only needed when you want to get the distribution of Comp Area):** | **6. top/bot (only needed when you want to get the distribution of Comp Area):** | ||
- | In the last line of top/bot files, even though it says [#frames per DCD] [#total frames], I believe they are actually both [#frames per DCD] [#frames per DCD], which are 1000 1000 for hypocotyl membrane. | ||
+ | //top file example// | ||
+ | ^Data in File ^ Meaning of Data ^ | ||
+ | |8|Number of Lipids Including Cholesterol| | ||
+ | |atomic-area.dat|Output atomic area file| | ||
+ | |lipid.dat|As Described in Step 5| | ||
+ | |0 150 1|min max and step size for area binning of sterol (must include even if no sterols)| | ||
+ | |0 150 1|min max and step size for area binning of lipids| | ||
+ | |sterol-top.dat|output sterol file (must include even if no sterols)| | ||
+ | |lip-top.dat|output lipid file| | ||
+ | |1000 1000|Step block size typically use # of frames in DCD file| | ||
Line 108: | Line 91: | ||
\\ | \\ | ||
The first file means first dcd file count in the following line, which is usually 1. \\ \\ | The first file means first dcd file count in the following line, which is usually 1. \\ \\ | ||
- | As explained in the comments inside test.scr, each values/name following test.csh are the follwing | + | As explained in the comments inside test.scr, each values/name following test.csh are the following |
- | # *.csh (# | + | < |
- | # note "dcd count" refers to number of files being read NOT ACTUAL DCD NAME (next argument) | + | # *.csh (# |
- | # SAME number for "first dcd" in ALL lines \\ | + | # note "dcd count" refers to number of files being read NOT ACTUAL DCD NAME (next argument) |
- | # "image atoms" = 9*(# | + | # SAME number for "first dcd" in ALL lines |
+ | # "image atoms" = 9*(# | ||
+ | </ | ||
'' | '' | ||
'' | '' | ||
Line 128: | Line 113: | ||
**>> area-a**: | **>> area-a**: | ||
- | **>> 2**: The lipid types of 2 are used instead of 8. (1-atom represented choline/ | + | **>> 2**: This is the dimension |
- | **>> | + | **>> |
**8. 2_run-dist-avg.scr**: | **8. 2_run-dist-avg.scr**: | ||
Line 140: | Line 125: | ||
**9. calc_avg_vertical.py & calc_avg_final.py: | **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 | + | 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. |
< | < | ||
# Update the number of each lipid component per leaflet in the same order as in area-a.inp | # Update the number of each lipid component per leaflet in the same order as in area-a.inp | ||
Nlist = [28, | Nlist = [28, | ||
</ | </ | ||
+ | |||
+ | **10. rtfpsf.str: | ||
+ | The file names in the rtfpsf.str file will most likely need to be updated. | ||
+ | |||
**Run the scripts:** \\ | **Run the scripts:** \\ | ||
Line 150: | Line 139: | ||
- | 1. Run script by command: 1_test.scr. \\ | + | 1. Run script by command: |
After run 1_test.scr (which may take about 0.5 ~ 2 hours), tmp and output files for all the dcd file count (1-35 in the example) will be generated. In each dcd count folder, atomic-area.dat will be generated which will have (#data points per dcd) rows and (# of represented atoms) columns. For hypo system here, atomic-area.dat has 1000 rows and 244 columns. | After run 1_test.scr (which may take about 0.5 ~ 2 hours), tmp and output files for all the dcd file count (1-35 in the example) will be generated. In each dcd count folder, atomic-area.dat will be generated which will have (#data points per dcd) rows and (# of represented atoms) columns. For hypo system here, atomic-area.dat has 1000 rows and 244 columns. | ||
- | 2. Get the averages and standard errors by command: 2_run-dist-avg.scr. You will see 2_avg_std_final.txt which contains the component area for each lipid type following the order in def_nlip.str. | + | 2. Get the averages and standard errors by command: |
+ | |||
+ | ** Ignore the rest of this wiki for now...Yalun will updated as needed ** | ||
**(Yalun: Following part to be updated)** | **(Yalun: Following part to be updated)** |
comp-sa.1596553084.txt.gz · Last modified: 2020/08/04 10:58 by edit