[gmx-users] Cluster pb

nicolas Dinter dinter at rc.m-kagaku.co.jp
Tue May 25 06:11:23 CEST 2004

Dr. Dallas Warren,

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

Nicolas Dinter
  -----Original Message-----
  From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]On Behalf Of Dallas Warren
  Sent: mardi 25 mai 2004 12:37
  To: Discussion list for GROMACS users
  Subject: Re: [gmx-users] Cluster pb


    So I am quite surprised by my results, could someone clarify my
    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

  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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040525/f6bf68c6/attachment.html>

More information about the gromacs.org_gmx-users mailing list