Using NAMD, I want to simulate aquaporin channel in POPC membrane. To induce the water flow, pressure difference across the membrane is needed. I am stuck with this point. Could you please suggest how to do it?
With NAMD you can apply all kinds of custom forces. I am sure you can solve this with TclForces there, but i think the NAMD mailing list if much more appropriate for those questions.
Anyhow, isn't it that diffusion through aquaporins is so fast that it does not need external forces?
see http://www.sciencemag.org/content/294/5550/2353.full.pdf
Hello.
Yes, the suggestion by Jan Majta can work. Create a two-system bilayer (POPC with aquaporin) and DMPC, for instance. Then, apply a pull force between both bilayers, reducing DMPC distance to POPC. The water layer between both bilayers will be slightly higher, probably enough to force water to pass through the aquaporin.
Ricardo
Build your system with AQP embedded in the membrane. Equilibrate as needed. Then use steered molecular dynamics to pull a water molecule through the channel. Once you get it started, water will move through AQP readily. There is no need for a two bilayer system, nor would using one achieve what you are trying to do.
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