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--- equilb_test [2026/07/24 12:53] – edit
+++ equilb_test [2026/07/25 13:16] (current) – edit
@@ Line 52: / Line 52: @@
 Change the initial guess (or your preference) for block size (in ns) and the steps size (in ns) of your output (usually 10ps, but make sure to match your xst freq. As a note, xstfreq=5000 means 10ps):
-  ./area_handling.py 10 0.01 >& all.dat
+<code>
+# the formula for step size in ns is xstfreq * timestep * 10^-6 (assuming timestep is fs/step)
+# Example: if xstfreq is 5000 and timestep is 2.0 (values located in dyn.inp) step size = 0.01
+./area_handling.py 10 0.01 >& all.dat
+</code>
 After running //pymbar_area_ka.scr//, you'll see //all.dat//, SA/lipid is in angstrom^2 and Ka is in N/m.
@@ Line 59: / Line 64: @@
 a) If you're getting segmentation faults, run ''conda update numpy''. This should fix the issue.\\
 b) Ensure that all geteq files are placed in the same directory as area_time_acc.dat and your other area_1_lipid files. There should not be a geteq subdirectory.\\
-c) If you see "Skipping 10 ns of equilibrium data," that is intended and not an error.
+c) If you see "Skipping 10 ns of equilibrium data," that is intended and not an error.\\
 d) If conda is returning a massive error report when trying to run ''conda create -n geteq python=3.9 numpy'', try running
 <code>
 conda clean --all -y
+# if that still doesn't work, run
 echo "number_channel_notices: 0" >> ~/.condarc
 </code>