[gmx-users] Cluster pb

David van der Spoel spoel at xray.bmc.uu.se
Wed May 26 09:32:31 CEST 2004

On Wed, 2004-05-26 at 01:15, Dallas Warren wrote:
> Nicolas,
> >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 
> downloadable.
> May be ask the GROMACS developers if they are considering improving the 
> random placement function in genbox?
This has quite low priority I'm afraid.

If you start out with low density you can however make it equilibrate by
coupling to a pressure of, say, 1000 bar. If you couple to 1 bar you
will find that equilibration is slow, because the difference between 0
bar (vacuum) and 1 bar is rather small compared to typical fluctuations.
Afterwards you will have to re-equilibrate at 1 bar of course.

> 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
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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