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--- surface_area_of_lipid [2021/05/25 14:26] – admin
+++ surface_area_of_lipid [2023/02/05 10:39] (current) – admin
@@ Line 9: / Line 9: @@
 This simple analysis is used to estimate the overall average surface area (SA) per lipid. If you are analyzing a single component membrane then this is equivalent to the component's SA/lipid. Otherwise, this is the average of all lipids.
-Those at UMD should use the DT2 path: **/lustre/jbklauda/scripts/area_1_lipid**
+Those at UMD should use the ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/area_1_lipid**
 Outside of UMD a sample script is given in the gzip file: {{ :area_1_lipid.gz |}}
@@ Line 82: / Line 82: @@
 The example states that you want to do the averages from the last 20 dyn*dcd files. Let's say you have 50 dyn*.dcd files, then the first 30 files are ignored. If each file had 2ns of data, then you are calculating the average from 60-100ns.
-.2 Calculate the block-average surface areas by command: ''./3_cal_avg_std.scr''
+.2 Calculate the block-average surface areas by command: ''./3_calc_avg_std.scr''
 **Note: **For  //#define MAX_R 1000000//  in area-block.c, you might have to change the number to a larger one (larger than your # data points) and recompile it.
@@ Line 90: / Line 90: @@
 .3 Standard Errors from Block Average
-Calculate averages, sample standard deviation, and standard error of block averages by command: ''./4_run_calc_stderr.scr''
+Calculate averages, sample standard deviation, and standard error of block averages by command: ''./4_run_calc_sterr.scr''
 The file //avg_stderr.dat// will be generated that will show the final values that we need, which are the average of the block averages and the standard error of the block averages, i.e. SA_avg/lip +- Standard error. You may refer to the attached Excel file which also demonstrate how the standard error is calculated if you are interested.