I have carried out MD simulations about membrane channel. In the process of MD simulations, the upper leaflet and the lower leaflet were separated as shown in figure 1. I tried to center the two leaflet together and used PBC wrap command in VMD "pbc wrap -centersel "resname PAP" -center com -compound res -all", PAP is the name of the fixed channel in the membrane. The two leaflets were together as shown in figure 2. When I evaluated the thickness of the membrane, something weird happened. The thickness of the membrane experiences great fluctuations from the time the two leaflets was taken apart. I guess there is something wrong in the treatment of PBC but I don't know how to tackle this problem.
Hi Lulu. If I understand correctly what you did, then it would seem that this is just sort of a bookkeeping error with the coordinate wrapping. When you say that the upper and lower leaflets were separated, I assume you mean that the picture (fig 1) is the result of wrapping the coordinates to the periodic box, along with some translation of the system in the direction perpendicular to the membrane plane; this makes it appear as if the upper leaflet is now "below" and separate from the lower leaflet, even though physically (via periodic boundaries) they are still in contact as always. What you need to do is re-wrap the coordinates according to a different origin, so that it still looks like an intact membrane (with the water on the outside, not in the middle) and then do your thickness calculations. In the future, you might want to run your MD simulations without wrapping the atom coords on output, and just do wrapping (if you want) afterward for visualization; this tends to simplify analysis. Hope this helps!
You're welcome! If only all problems were so easily fixed. :)
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