[gmx-users] introducing a molecule into a bilayer
David L. Bostick
dbostick at physics.unc.edu
Mon Aug 8 18:34:05 CEST 2005
Probably the best way to do this is to start with an unequilibrated bilayer
... i.e. build it from scratch with straight chained lipids the old
fashioned way. This can be done with genconf and a model of each lipid
species in the bilayer. You will need to build each lipid model with some
modelling program. Then you can generate monolayers with genconf, giving
each lipid a random rotation around the z axis. Then generate a slab of
water above and below the bilayer with genbox and editconf... I believe
there was a paper by Parag Mukopadhyay (sp?) and Peter Tieleman in Biophys.
J. explaining how to do it. I think it was POPS bilayer with salt, but I'm
Trying to put your lipid into an existing equilibrated bilayer can be
difficult if the new lipid does not resemble the ones that are already
there. Also, you will have to equilibrate it all over again anyway, so why
not start from scratch? Anyways, this is my opinion. good luck!
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Mon, 8 Aug 2005, Ramachandra Rao Gullapalli wrote:
> Dear GMX ers
> I have a question for which i have tried in vain to find an answer in the
> archives. I am running a bilayer simulation, and i would like to introduce a
> lipid like molecule into the bilayer. I have made the .itp file for this
> molecule, and i have the bilayer from Dr Tieleman s website including the pdb
> Can anyone give me pointers on how to go about this? There was an old message in
> archives which says that i should grow the molecule into the bilayer. I am not
> quite sure what it means.
> Also, can i remove one lipid molecule from the bilayer, and introduce the
> molecule? im not sure how i would go about the coordinates though.
> I sincerely look forward to receving a reply from the group.
> Thanks for your time
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
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