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--- equilb_test [2023/06/07 17:17] – admin
+++ equilb_test [2026/07/25 13:16] (current) – edit
@@ Line 1: / Line 1: @@
 ==== Get the equilibrium data (test) ====
-(author: Yalun Yu,  email: alanyu17@terpmail.umd.edu / yalun.research@gmail.com)
+(main author: Yalun Yu,  email: alanyu17@terpmail.umd.edu / yalun.research@gmail.com) \\
+(updates: Joshua Lucker, email: jlucker1@umd.edu)\\
+(Error handling updates: Eric Zhang, email: ezhang32@umd.edu)\\
-< Email me if anything is wrong >
+< Email jlucker1@umd.edu if you have any questions about this wiki page >
 This is a brief instruction to obtain the time range of equilibrium (and also the minimum block size can be used for standard error calculation). Calculation of SA/lipid and Ka is done automatically for your lipid only system. Make sure you run the //1_run_area.scr// script from [[Surface Area of Lipid]] before doing this section. Please put the scripts listed in this wiki in the same folder as you run //1_run_area.scr//. You will need pymbar package (in python) for this:
-. Install Anaconda (https://www.anaconda.com/distribution/).
+. Install Anaconda (https://www.anaconda.com/download).
    a) Download the python3.7, python3.9 or lastest version for Linux [I used the '64-Bit (x86) Installer']
    and put the .sh installer in your home directory (or any other place you can access and execute it) on ZT1.
@@ Line 49: / Line 51: @@
    nlip=36
-Change the initial guess (or your preference) for block size (in ns) and the steps size (in ns) of your output (usually 1ps, but make sure to match your xst freq):
+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 0.001 >& 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.
+**Warnings / Error Handling**\\
+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.\\
+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>