On Wed, Apr 23, 2008 at 03:22:09PM +0400, Vasilii Artyukhov wrote: > > I'm afraid I have to use TIP5P; I _am_ looking at temperature dependent > information, and also, I need a good description of hydration of small > molecules I mentioned. These and other considerations make more or less > every other water model I know of (including TIPxP-Ew) at least twice less > attractive than TIP5P. So if TIP5P doesn't screw up the description of the > membrane as much as any other model would the water part, I think it will > do.
if you could share your (future) experience with tip5p and membranes with us, that would be great. some time ago i decided to switch to all-atom simulations, and then had to make the choice between tip4p and tip5p. now for the life of me i don't remember *why*, but i do know that there were some strong arguments against tip5p. > 2008/4/22 Marc F. Lensink <[EMAIL PROTECTED]>: > > > > i'm very happily using berger/oplsaa/tip4p. mind that this means ua > > lipid tails and the rest aa, so unless you have a distinct lipid > > phase, it's probably not what you want. personally i'm not (yet) > > convinced it's a better combination than berger/gromos/spc, though. > > I'm sorry, I didn't quite understand the argument about 'having a distinct > phase'. Could you please elaborate? suppose there's a protein in your bilayer. if the lipids tails are berger, ie united-atom (ua), but the rest of the system, most importantly protein, is all-atom (aa), then you have an ua-aa contact region, which the force field is not parameterised for. i'd like to add that this is not necessarily a problem. current-day united-atom force fields already have ua-aa contacts when they use explicit hydrogens for polarised hydrogens (SOL, PHE, etc). > So, this leaves us with two votes for Berger/TIP4P and nothing at all about > CHARMM27. But it would be really nice to hear from someone who'd been using > the latter FF. (I realize that it might be smarter to ask such questions on > the CHARMM forum, but on the other hand, I'm still willing to do this in > GROMACS...) i hear very good stories about the charmm27 lipid tail parameters, but haven't used them myself. keep in mind that you will typically have to use surface tension terms to keep a correct area per lipid. not too long ago new dppc head group parameters were published, for use with charmm27, that do not require this surface tension term: Biophys J (2007) 92:4157. worth to check out, i'd say. cheers, marc _______________________________________________ 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
