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asymmetric_bilayer

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asymmetric_bilayer [2022/08/24 09:53] – [Step 1: generate monolayers] editasymmetric_bilayer [2026/03/04 00:09] (current) – [Package and operation] edit
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 Contact email: mkhsieh1027@gmail.com \\ Contact email: mkhsieh1027@gmail.com \\
  
-(The package was constructed based on bacterial inner membrane models with phospholipids; the system with steroid lipids and proteins have not been tested yet. Please provide comments and feedbacks to improve this package. Thanks.)+**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):**\\ 
 +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. 
      
 The **asym_memb_builder** is used to generate an asymmetric lipid bilayer from two symmetric bilayers by manipulating the smaller monolayer to match the size of the larger monolayer if the size if very different (more than 5%). The package is adapted from the scripts of CHRAMM Membrane Builder, having 5 sequential steps to build a simulation box of asymmetric membrane with explicit water and ions. Briefly, after checking the input symmetric bilayer information (Step1.0) and isolating lipid, water, and ion of each leaflet (Step1.1), the script provides the potential enlarged monolayers (Step1.2) for user’s selection and recreate a half simulation box with lateral waters and ions from original molecular structure in the input symmetric membrane system (Step1.3). The asymmetric bilayer is generated at Step2 using the original input molecular structures. The simulation box size is checked at Step3 and the concentration of KCl could be modified by editing step3_size.str if user would like to update it. The asymmetric bilayer will be rechecked and isolated by individual segment (lipid, water, and ion) at Step4.1; the water box is directly adapted from the original input without change (inactive the Step4.2); and the number of ions for neutralizing system or matching the updated KCl concentration is processed at Step4.3. Then, all the updated segments (lipid, water, and ion) are assembled at Step5.1, and the input files of the asymmetric bilayer is prepared for NAMD at Step5.2. As usual CHARMM-GUI practice, the simulation is followed by step6 equilibrium and step7 production runs. \\ The **asym_memb_builder** is used to generate an asymmetric lipid bilayer from two symmetric bilayers by manipulating the smaller monolayer to match the size of the larger monolayer if the size if very different (more than 5%). The package is adapted from the scripts of CHRAMM Membrane Builder, having 5 sequential steps to build a simulation box of asymmetric membrane with explicit water and ions. Briefly, after checking the input symmetric bilayer information (Step1.0) and isolating lipid, water, and ion of each leaflet (Step1.1), the script provides the potential enlarged monolayers (Step1.2) for user’s selection and recreate a half simulation box with lateral waters and ions from original molecular structure in the input symmetric membrane system (Step1.3). The asymmetric bilayer is generated at Step2 using the original input molecular structures. The simulation box size is checked at Step3 and the concentration of KCl could be modified by editing step3_size.str if user would like to update it. The asymmetric bilayer will be rechecked and isolated by individual segment (lipid, water, and ion) at Step4.1; the water box is directly adapted from the original input without change (inactive the Step4.2); and the number of ions for neutralizing system or matching the updated KCl concentration is processed at Step4.3. Then, all the updated segments (lipid, water, and ion) are assembled at Step5.1, and the input files of the asymmetric bilayer is prepared for NAMD at Step5.2. As usual CHARMM-GUI practice, the simulation is followed by step6 equilibrium and step7 production runs. \\
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 ====== Package and operation ====== ====== Package and operation ======
 For DT2, the package at /lustre/mhsieh/asym_memb/asym_memb_builder_v4 \\ 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 \\  Authors: Min-Kang Hsieh and Jeffery B. Klauda \\ 
 \\ \\
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 2. **step2_gen_bilayer.str**: Parameter table of the generated bilayer \\ 2. **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 ==== ==== Step 3:   Determine size of simulation box ====
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 **Step5.2: Generate NAMD input** \\ **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** \\ CHARMM configuration file:  **step5.2_input.inp** \\
 Output files: ./namd directory \\ Output files: ./namd directory \\
asymmetric_bilayer.1661349220.txt.gz · Last modified: 2022/08/24 09:53 by edit