I am running a 30 ns membrane protein simulation in Desmond using DPPC as the lipid bilayer. What sort of analysis can be performed?
The better question is: why are you running the simulation? You can spend lots of time "doing analysis," but ultimately they should answer some scientifically relevant question.
Hi,
Bilayer thickness, radial distribution function, atomic density profile, area per lipid, lateral diffusion of the lipids, order parameters, ....
Norbert
The better question is: why are you running the simulation? You can spend lots of time "doing analysis," but ultimately they should answer some scientifically relevant question.
Depends on what properties you are looking for. For the protein part, you can look at the stability of the structure in terms of RMSD, conformational change of the structure, etc; for the membrane part, you can look at what Norbert suggests; besides, you could look at protein-lipid interactions (hydrogen bonding network or vdW packing) or ion conductance through an ion channel.
Whatever you're doing, if the simulation includes the protein, membrane (between 100 and 300 molecules) and explicit water (thousands of molecules) a run of 30 ns does not have much meaning. You must get at least 100 ns, because there are many events that can alter the simulation (destruction of the membrane, alteration of the protein structure, etc.), So you must be sure that the architecture of the model is intact on a large scale.
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