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Nicolas,<br><br>
<blockquote type=cite class=cite cite>So I am quite surprised by my
results, could someone clarify my situation?<br>
How can I prevent cluster from forming?</blockquote><br>
You are aiming to get pure liquid benzene, right? In the second
case, what was your density? By clustering, it sounds like that you
have some areas of the box with no molecules, i.e. it is a vacuum.
Running the simulation for longer with the pressure coupling will
eventually eliminate that.<br><br>
In setting things up for something like this, I distribute my molecules
in a box that is about twice the volume it is meant to be.
Distribute them throughout the box, then scale the box dimensions using
editconf, then run the EM etc.<br><br>
Also, what are you using to distribute the molecules throughout the
box? Not sure how it is with the current versions, but I use to use
genbox but it would generate way too many clashes/overlaps between
molecules and atoms to be of much use at all. Now I use a program
that someone here wrote that does a far better job of random
distribution.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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