> Dear GMX users, > > I'm interested in calculating non-projected area/lipid of huge bilayer > with undulations. I think that if the bigger solvent probes were used, > the non-projected area per lipid may be reasonably calculated from the > solvent accessible surface area because solvent probes cannot be > inserted between lipid headgroups, which will avoid overestimation of > area per lipid. So, I'm testing this with small bilayer (128 lipids) > using g_sas, and have some questions. > > 1) If the bigger solvent probes (such as -solsize 1.7 or so) are used, > SASA of lipid will become smaller, but should be always bigger than the > XY-area of this small bilayer system. But, when I increased the value > of -solsize, SASA becomes even smaller than the XY-area at some point. > In this case, how can SASA be smaller than XY-area of the bilayer?
How are you measuring XY-area? What periodicity are you using? > 2) The manual says that -ndots is related to accuracy, but when I tried > different values, I don't see trends of increase or decrease. Could > you tell me what it is and what the reasonable value will be? > > 3) I saw SASA fluctuate quite a lot. Is there any way to decrease > fluctuation? Fluctuating with what? Mark _______________________________________________ gmx-users mailing list [email protected] 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
