[gmx-users] question about genbox

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 2 06:24:51 CET 2005

Hi Sven,

Just to add a word on Dallas' reply. Use a larger box, such that you get
just over the number of water molecules you need. Then delete the surplus.
Pressure coupling will fix the vacuum.



On 11/2/05, Dallas B. Warren <Dallas.Warren at vcp.monash.edu.au> wrote:
> Sven,
> > I'm trying to solvate 200 molecules of Glycine in water and I need a
> > certaine concentration in the box. How can I determine the
> > number of water
> > molecules to be added to the glycine. when I run the genbox
> > command it gives
> > me 1712 water molecule and I need them to be 2650 instead.
> Couple of options, save a smaller number of waters in a gro file and
> tell genbox to add the correct number of those (not sure if it has
> improved, but this script use to get some molecules overlapping and with
> bad contacts, so take care). Or adjust the dimensions of the box using
> editconf until you get the correct number of water molecules added when
> you solvate it.
> Catch ya,
> Dr. Dallas Warren
> Lecturer
> 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 9073
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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