Re: [gmx-users] Re: Measure contour area of bilayer undulation
Hi, > > > My point was rather the opposite - when people measure area/lipid in the > lab on bilayer slabs there will be undulations present since they are > typically not under tension. We discussed this with John Nagle a couple of > years ago, and came to the conclusion that you should not try to compensate > for it. This is one of the reasons you get more accurate results for larger > systems. > I'm afraid this is an oversimplification of the problem. In order to obtain an accurate electron density profile of the membrane you need at least 3 to 4 orders of X-ray diffraction. For this, it is needed a non-zero tension by means of an applied osmotic pressure. The tension-free state is extrapolated from an osmotic pressure curve. I think Hwankyu is right in his questioning. Maybe a better approach is to simulate the membrane system in a constant area ensemble in several values of average area per lipid. You can, then, compare your simulated structures with the experimental one and choose the "better" one. This is not my idea. It has been done before in the same Nagle group. Regards. Pedro. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Measure contour area of bilayer undulation
Hi, On Aug 31, 2007, at 11:02 PM, Hwankyu Lee wrote: Thank you very much for your suggestion in the gromacs forum, but I may not understand your explanation completely. In the small bilayer, there is no fluctuation, so area/lipid can be calculated based on the cell dimensions. But, in the big bilayer, area/lipid can be much larger than that obtained from XYarea/lipid number because of undulations. First, try to keep the discussions on the list so the answers make it to the archive :-) Could you explain more details about reasons that area/lipid in the big bilayer can be calculated better based on cell dimensions? My point was rather the opposite - when people measure area/lipid in the lab on bilayer slabs there will be undulations present since they are typically not under tension. We discussed this with John Nagle a couple of years ago, and came to the conclusion that you should not try to compensate for it. This is one of the reasons you get more accurate results for larger systems. If you still want to derive it (the error is in the order of 1%, IIRC) you should start with the works of Nagle & Safran! Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
