[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa
chris.neale at utoronto.ca
Mon Apr 21 17:30:54 CEST 2008
I use tip4p/opls/berger combination and it works well for me. I have never used tip5p. I suggest that you build your membrane and run
one control simulation (sounds like you would lean toward using spc for this) and then one simulation with tip5p. Check order parameters and
area per lipid while using anisotropic pressure coupling. You should be able to fine protein-water combination information in the
literature. I suggest that you run these tests for >>10ns each. With a modest cluster you should be able to get ~15ns per week per system
if you run them on NP=4 and keep your system relatively small. I have never seen a paper dedicated to combining different water/protein/lipid
ff's but if you do find one (or write one) there are many people here who would be interested to read it.
Also, are you sure that you want to use tip5p? Unless you are looking at temperature/pressure dependent information or
really need to nail the diffusion constant then I would suggest tip4p/3p or perhaps the tip4p-Ew from Horn, Swope, Pitera,
Madura, Diak, Hura, and Head-Gordon. For a very nice review or water models look at Bertrand Guillot J mol. liquids. 101/1-3 (2002) 219-260.
Dear GROMACS users,
particularly, those experienced with membrane simulations,
I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain
small solutes, much like what was done in A.K. Sum & J.J. de Pablo, Biophys.
J. 85, 3636 (2003) with DMSO. I'd like to use the TIP5P and OPLS all-atom
parameters for water and other stuff, but there's still the question of what
parameters to use for lipids. I'm aware that I'm supposed to do my own
research on this matter, but it'd still be very nice to have some advice on
the choice of parameters from someone with more experience in these things.
>/From what I've managed to figure out of Erik Lindahl's tutorial on the
/website, I'm basically encouraged to use either Berger parameters, or the
CHARMM27 forcefield (btw, the ffcharm files aren't present on the new
website, had to search the mailing list for a link to the old version) -
unless I know very well what I'm doing, which I obviously don't presently :)
Berger seems to be commonly used in combination with OPLS; however, I get
the impression that it's supposed to work best with SPC, which doesn't suit
my needs really well. As for CHARMM, I'm not really sure if it's supposed to
mix well with OPLS for solutes, and it also seems to be parametrized for use
with TIP3P, not 5P.
So, if anyone could comment on the above questions or point out some of my
misconceptions, this would be greatly appreciated! :)
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