On Fri, Mar 12, 2010 at 10:06:53PM -0500, chris.ne...@utoronto.ca wrote: > > Note that the "Berger" lipids were in fact developed by many people > and they have come to be named by only one of the contributors. The > reference that I use for my 1/8 scaling of the LJ 1-4 is: > > Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and > thickness fluctuations in lipid bilayers from molecular dynamics > simulations. Biophys. J. 79:426?433. > > where they state in the methods: > > "1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4 > Lennard?Jones interactions a factor of 8." > > I believe that this idea originated in a Jorgensen paper looking at > bulk simulations of n-alkanes, but ashamedly I can't recall for sure > at this moment. If you need it, I can look it up next week (let me > know).
And since we're quoting; From: Langmuir 2009;25:5230 "Nonbonded parameters (sigma and epsilon) between OPLS/aa head group atom and Berger acyl chain 1-4 pairs are scaled by a factor 8 as recommended [opls]" [opls] JACS 1988;110:1657. cheers, marc -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
