[gmx-users] Re: set up self assembly for mixture of lipids using genbox

maria goranovic mariagoranovic at gmail.com
Tue Feb 3 16:56:27 CET 2009

That sounds like a good idea. However, what sort of "cheap physical model"
are you suggesting to get rid of the very ordered initial state ?


> maria goranovic wrote:
> > Hello
> >
> > I am trying to using genbox to set up a random 2-lipid mixture. Is there
> > a way to do this? First, i put 100 POPC molecules randomly in the sim.
> > box. Now I want to add 28 POPS lipids. How can I do this ?
> I'm not aware of a direct method for doing this. Creating interstices
> for arbitrarily shaped molecules is non-trivial.
> One approach is to choose your lipid mixture and to concatenate
> cunningly-sized boxes each with a pure sample of one component of the
> mixture. Then a long equilibration will see the mixtures randomize. You
> can probably get away with a long "pseudo-equilibration" period with a
> very cheap physical model to make sure you get away from the highly
> ordered state, then a shorter "real" equilibration to move into the
> right ensemble from that intermediate point.
> Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090203/b1e131fd/attachment.html>

More information about the gromacs.org_gmx-users mailing list