Welcome to the help page of MemBuilder II
MemBuilder II is provided to generate initial structure of both homogenous and heterogeneous lipid bilayers,
micelles, and liposomes.
The source code is written by C++ and the Web Interface is written using PHP and Java Script.
Users on MemBuilder II can specify type and concentration of lipid molecules to build desired membranes.
MemBuilder II supports forty different lipid molecules based on six different force fields
including all-atom and united-atom force fields that can be selected upon users' request.
MemBuilder randomly places selected lipids to build the whole membrane and then performs energy minimization at the presence of
water and ions to decrease local stresses inside the lipid bilayer that will take a few minutes according to the system size.
This web server helps GROMACS users to generate input files necessary to
build a membrane system for molecular dynamics simulation.
Please pay attention that you need to:
Download Gromose43a1-s3, slipid-amber, charmm-27, and charmm-36 force field sources
from the download page and put them into the installed GROMACS directory.
By default you can find the appropriate directory at /usr/local/gromacs/share/top.
Download topology file (.itp) for each selected lipid molecule and
put in your working directory or any other directory that GROMACS can find them.
MemBuilder II runs 16 different stages of minimization on the constructed bilayer,
micelle or liposome in vacuum to eliminate all clashes; however,
you may need to carry out further minimization in your local computer according to your purpose.
MemBuilder II uses a different seed number to support randomness for each trial.
If you find the distribution of different lipids NOT appropriate,
please try once again with the same lipid type and composition to find your desired lipid distribution.