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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