[gmx-users] Cluster pb

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue May 25 05:37:23 CEST 2004


>So I am quite surprised by my results, could someone clarify my situation?
>How can I prevent cluster from forming?

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.

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.

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.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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