I have a pdb file of coarse grained lipid monolayer system consisting of 64 DPPC lipids. The pdb file is missing box information. I am interested in simulating nanoparticle penetration in monolayer and this system require more than 2500 lipids. Membrane builder and Martini builder in CHARMM-GUI have size limitations. Is there a way to replicate the lipid molecules in GROMACS? How do we define the initial box for the monolayer with 64 lipids in order to increase the number of lipids in the system?
I assume that packmol package is suitable in your case. Just install a packmol and find attached other pdb file and input file. Using those files you can easily create any size of pdb file. Initializing command is: packmol < bilayer-comment.inp
If you have question just let me know.
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