Well I know that the x/y directions are scaled isotropically and the z direction is scaled independiently, and i must give just 2 compresibility valors, but people don't give this valor in the most of the papers about membrane simulations. For example i use on DPPC membrane compressibility =4.5e-5 4.5e-5 ref-p = 1.0 1.0
the area change from 0.64 to 0.62. When i use the same parameter on POPG or POPC bilayer the system is exploding. If i change to on POPC and POPG compressibility =1.0e-5 4.5e-5 ref-p = 1.0 1.0 it gives areas about 0.639 (POPC) and 0.53 (POPG). The POPG area is according to "Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys J. 92, 1114-1124 (2007), and I'm using the same temperature. But the POPC area isn't good. My questions are: Can i use compressibility =0 4.5e-5 and ref-p = 0 1.0 on peptide-membrane systems? (at first the peptide is about 10 A to the bilayer interface and after it's inserting in the membrane) What are the correct valors for the compressibility on membrane systems? Thanks a lot, Maité On Nov 24, 2007 10:27 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi: > > > > I am working on membrane simulation under lipid (DPPC, from Peter > > Tieleman group site). I equilibrated dppc membrane for 10 ns and when > > i got the area by lipid (x*y/ # lipids) using g_energy, i obtained > > that the area is constant (0.64), there isn't any fluctuaction during > > 10 ns..althougth the volumen isn't constant. > > What's wrong in this simulation? > > Did you notice that your box dimensions are not changing in X and Y > directions? Do you understand what semiisotropic pressure coupling does? > > Mark > > > _______________________________________________ > gmx-users mailing list gmx-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 mailing list gmx-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
