Hi Stephen, > I am particularly interested in lipid .rtp libraries hopefully for something > that has all-atom force fields, as I personally believe simulations should be > as real as possible, and also believe non-polar hydrogens still illicite some > force in the overall scheme of the molecular simulation.
Yes, of course they do. And don't forget charge transfer effects, polarization and quantum effects. But you can't have it all. Every model has its domain of application and its pros and cons. > As most lipid systems in cells are insanly complec, many lipid types in many > proportions and chain lengths, etc... I woundered if somone(s) has already > constructed a library with the 200 or so outer membrane lipids. I did read > years back about mitochondrial simulations, which did include dozens of > lipids, even cardiolipin, etc...but never found libraries. References would be good. I know there's a good deal of effort on parameterization of lipids, especially in the group of Tieleman, as well as in ours. But an encompassing library of lipid models seems to be a bit too much to ask for at the moment. Parameterization is a tricky process, especially if the experimental data on pure lipids and controlled mixtures is scarce. Any such library should be used with caution, i.e. with background reading of the methods and assumptions used for the parameterization. > Happy Ascention Errm, I wasn't intending on going yet... :p Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
