I want to find out the interaction between polymer and cell membrane like membrane permeability, and chemical interaction between polymers and membranes and other parameters. I can use liposomes as a model membrane. Can anyone suggest a suitable software for this?
Is there any such software available free of cost?
http://pubs.rsc.org/en/Content/ArticleLanding/2014/CP/C3CP54242D#!divAbstract
The first question you should ask is not about the software but about the model you want to use. Polymer-membrane interactions can be quite complicated, depending on what it is you wish to study. Things that matter are, for instance: Is the polymer stiff or flexible? Is it hydrophilic or hydrophobic? Is it maybe amphiphilic? Does it show nontrivial structure formation, such as polypeptides would? How long is it? Etc. Depending on answers to these questions, the approach can vary from using a simple paper-and-pencil calculation to answer your question to abandon-all-hope because you can't do it with currently available tools.
Hello Dr. Markus.
The polymer is a polyampholyte. Its slightly hydrophobic also. The molecular weight is around 5 kDa. And as far as i know, it doesn't show any nontrivial structure.
5 kDa is pretty big. This also means that the membrane ought to be made pretty big, since you presumably do not want the adsorbed polymer to see its periodic images. Given that, I suspect that there's no way to simulate this atomistically. Instead, it might be possible to use coarse grained models, maybe MARTINI, which is conveniently implemented in Gromacs. But before you set this up, try a few order of magnitude estimates: What is the radius of gyration of that polymer in solvent? What would it be in the membrane? What would it be if it gets 2-dimensionally confined on or in the membrane? How big would therefore the membrane have to be? How many lipids, how many waters, etc. What do you think would be the equilibration time of the system (presumably huge)? And hence, how long would you have to simulate? Do you have the resources to do so? If not, can you make the polymer smaller? Or the model more coarse-grained?
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