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--- asymmetric_bilayer [2022/08/24 09:56] – [Asymmetric membrane builder] edit
+++ asymmetric_bilayer [2026/03/04 00:09] (current) – [Package and operation] edit
@@ Line 6: / Line 6: @@
 Contact email: mkhsieh1027@gmail.com \\
-Update:
+**Update (02.15.2026):**\\
-The package (v4) was constructed based on bacterial inner membrane models with phospholipids; the system with other lipids should use v5 and the system with proteins should use a limited version asym_memb_builder_v4_prot . Please provide comments and feedbacks to improve this package. Thanks.
+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):**\\
+The package (v4) was constructed based on bacterial inner membrane models with phospholipids and the system with other lipids should use v5. \\
+The packages may not be able to apply to system with glycolipids.
+The system with proteins should use a limited version asym_memb_builder_v4_prot . \\
+Please provide comments and feedbacks to improve this package. Thanks.\\
+In step5.2, one should be able to create input for several MD simulation packages by Force Field Converter at CHARMM-GUI page (https://charmm-gui.org/?doc=input/converter.ffconverter)
+where takes the step5_assembly.psf and step5_assembly.crd file generated from step5.1 with step5_assembly.str information.
@@ Line 15: / Line 23: @@
 ====== Package and operation ======
 For DT2, the package at /lustre/mhsieh/asym_memb/asym_memb_builder_v4 \\
-or download the package through the link {{ :asym_memb_builder_v4.tgz |}} \\
+/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 |}}  {{ :asym_memb_builder_v5.1.tgz |}}\\
 Authors: Min-Kang Hsieh and Jeffery B. Klauda \\
 \\
@@ Line 163: / 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 ====
@@ Line 207: / Line 217: @@
 **Step5.2: Generate NAMD input** \\
+**Update:**\\
+One should be able to create input for several MD simulation packages by **Force Field Converter** at CHARMM-GUI page (https://charmm-gui.org/?doc=input/converter.ffconverter) \\
+where takes the step5_assembly.psf and step5_assembly.crd file generated from step5.1 with step5_assembly.str information.
 CHARMM configuration file:  **step5.2_input.inp** \\
 Output files: ./namd directory \\