[gmx-users] Cluster pb

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed May 26 01:15:14 CEST 2004


>Yes, I am trying to get the pure liquid benzene. I will try to do longer 
>simulation and see.
>I tryied to run a EM with the 5*5*5 box, and use editconf to reduce the 
>box size, or in an other try with the density option but clusters remain.

Sounds like the box is still too large for the number of molecules in it, 
hence the appearance of clusters.

What is the density you are getting?

>Could you tell me more about this program please, is it  downloadable?

It is something that a colleague here wrote in house.  Sorry, it isn't 

May be ask the GROMACS developers if they are considering improving the 
random placement function in genbox?

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.

More information about the gromacs.org_gmx-users mailing list