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--- asymmetric_bilayer [2022/08/25 17:03] – [Asymmetric membrane builder] edit
+++ asymmetric_bilayer [2026/03/04 00:09] (current) – [Package and operation] edit
@@ Line 5: / Line 5: @@
 Created by Dr. Min-Kang Hsieh \\
 Contact email: mkhsieh1027@gmail.com \\
+**Update (02.15.2026):**\\
+The update (asym_memb_builder_v5.tgz) reflects the corresponding modification of ion residue names in IONS, replacing the POT and CAL resnames. In Step 6, phosphorus atoms are constrained in step5_input.ref following CHARMM minimization. Using the helper file (./namd/membrane_lipid_phos_restraint.namd.str), users can modify the constraint settings as needed.
 **Update (08.24.2022):**\\
@@ Line 22: / Line 25: @@
 /lustre/mhsieh/asym_memb/asym_memb_builder_v5.beta \\
 /lustre/mhsieh/asym_memb/asym_memb_builder_v4_prot \\
-or download the package through the link {{ :asym_memb_builder_v4.tgz |}} {{ :asym_memb_builder_v5.beta.tgz |}}\\
+or download the package through the link {{ :asym_memb_builder_v4.tgz |}} {{ :asym_memb_builder_v5.beta.tgz |}}  {{ :asym_memb_builder_v5.1.tgz |}}\\
 Authors: Min-Kang Hsieh and Jeffery B. Klauda \\
 \\
@@ Line 170: / Line 173: @@
 . **step2_gen_bilayer.str**: Parameter table of the generated bilayer \\
 \\
-In step 2, the two monolayers listing in the input file (**step2_opt_a.str** or **step2_opt_b.str**) are combined to form a bilayer. If there is no adding lipid needed, step2a_gen_bilayer.inp is used with step2_opt_a.str as the input; otherwise, step2b_gen_bilayer.inp is used with step2_opt_b.str as the input. The centers of mass (COM) of both monolayers line on the z-direction. \\
+In step 2, the two monolayers listing in the input file (**step2_opt_a.str** or **step2_opt_b.str**) are combined to form a bilayer. If adding lipids, step2a_gen_bilayer.inp is used with step2_opt_a.str as the input; otherwise, step2b_gen_bilayer.inp is used with step2_opt_b.str as the input. The centers of mass (COM) of both monolayers line on the z-direction. \\
 \\
 ==== Step 3:   Determine size of simulation box ====