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 ? <br><br>-Maria<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
maria goranovic wrote:<br>
> Hello<br>
><br>
> I am trying to using genbox to set up a random 2-lipid mixture. Is there<br>
> a way to do this? First, i put 100 POPC molecules randomly in the sim.<br>
> box. Now I want to add 28 POPS lipids. How can I do this ?<br>
<br>
I'm not aware of a direct method for doing this. Creating interstices<br>
for arbitrarily shaped molecules is non-trivial.<br>
<br>
One approach is to choose your lipid mixture and to concatenate<br>
cunningly-sized boxes each with a pure sample of one component of the<br>
mixture. Then a long equilibration will see the mixtures randomize. You<br>
can probably get away with a long "pseudo-equilibration" period with a<br>
very cheap physical model to make sure you get away from the highly<br>
ordered state, then a shorter "real" equilibration to move into the<br>
right ensemble from that intermediate point.<br>
<br>
Mark<br>
<br>
<br></blockquote></div><br>