[gmx-users] lipid simulations

Anupam Nath Jha anupam at mbu.iisc.ernet.in
Sat Aug 18 20:12:55 CEST 2007


thanks for such a brief reply..
i have already downloaded these four files from the Peter Tieleman's
"dppc128.pdb  dppc.itp  inflategro.pl  lipid.itp"

but it looks like it has been simulated in water box for some time..
am i right? (i am afraid that i will not)
then what's next and what will be the *.mdp file for this simulation.


>> what parameters should I use for lipid simulations
> That depends on the forcefield that you are using. I will tell you
> about what I do but this is a poor substitute for what you should
> really be doing, which is:
> 1) find the initial paper that publishes the forcefield that you are
> using and figure out how they used it
> 2) Find some very recent papers that use this same forcefield and
> figure out how they use it and then read the relevant papers that they
> reference in their methods section.
> That said, I use the forcefield having a united atom representation of
> lipids originally proposed by Egberts et. al. (1994), with the charges
> from Chiu et. al. (1995), adjusted by Berger et. al. (1997), and with
> the additional scaling of 1-4 coulombics introduced by Lindahl and
> Edholm (2000). You can download these topologies from Peter Tieleman's
> website:
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
> It is common to use a twin range cutoff with LJ calculated every step
> up to 1.0nm and up to 1.4nm every 10 steps when the nonbonded list is
> updated. Coulombics are in real space below 1.0nm and by PME beyond.
> Pressure coupling is a semiisotropic berendsen barostat with tau_p of
> 4.0ps. Temperature is coupled to a berendsen thermostat separately for
> i)lipids ii)water+ions iii)protein witha tau_t of 0.1ps. I use lincs
> to constrain all-bonds.
> Note that I personally reduce the short range interaction cutoff to
> 0.9nm from 1.0nm. But you would be better to stick with parameters
> that are in more common usage.
> The protein forcefield that I use is opls-aa and I use tip4p water.
> When combining these forcefields, I use an unpublished method to scale
> 1-4 coulombics differently for protein and lipid:
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
> There are also a variety of related posts that come after that one but
> I can't remember what they are. You are going to need to do some
> searching.
>> how to insert the protein in that bilayer.
> You can either use the make_hole version of mdrun available for
> download from the user contributions section of the gromacs web site
> of a program called inflategtro available from Peter Tieleman's
> website: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
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