[gmx-users] question about genbox

[Tsjerk Wassenaar]

Hi Sven,

1. Before using genconf, make the box for one glycine larger. If you have a
distance of 0.5 nm to the wall originally, you will allow about four layers
of water between any two adjacent glycines.
2. As has been stated before, simulating for a short while will allow the
solution to randomize.
3. Making your box larger has nothing to do with your cutoff.

Cheers,

Tsjerk

On 11/2/05, Sven Huttenhouse <mdsimulation at hotmail.com> wrote:
>
>
> 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
> this?
>
> 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
> Sven
>
> >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.
> >
> >Cheers,
> >
> >Tsjerk
> >
> >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.
> > > _______________________________________________
> > > gmx-users mailing list
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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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--

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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