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 > 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 > > >
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