[gmx-users] question about genbox

Sven Huttenhouse mdsimulation at hotmail.com
Wed Nov 2 17:57:52 CET 2005

Thank you all for your reply
actually I genarated 200 glycine molecules by replicating one molecule using 
genbox abd it gave me molecules that are randomly disrtibuted but attached 
to each other. I then used genconf to generate the the molecules and it gave 
me 200 molecules that are not attached but also not randomly distributed. 
When I use editconf to generate a box aroud the molecules (generated by 
genconf) and then genbox to solvate them in water I notice that water 
molecules are located around the 200 molecules and no water molecules comes 
withen the 200 glycine molecules.
what I'm looking for is to get 200 glycine molecules not attached to each 
other and randomly distribulet in a box of water molecules. How can I get 

One more thing, when I change the bex dimentions using option -d in editconf 
this will affect the cutoff distance is this ok?

kind regards

>From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] question about genbox
>Date: Wed, 2 Nov 2005 06:24:51 +0100
>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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