Hi Maite,
You can copy the file vdwradii.dat from the $GMXDIR/share/gromacs/top/
directory and change the vdwradii for the carbon or oxygen atoms. This
way, more waters would be rejected because of overlaps when solvating
the system using genbox (genbox -h). Alternatively, there is a script
somewhere (somehwere on my harddisk even) to remove water molecules
from inside a membrane, using pymol. On the other hand, it wouldn't
take very long for water molecules to be rejected from the hydrophobic
environment of the lipid tails, so a short MD run may be of use.
Hope it helps,
Tsjerk
On 3/14/07, maite lopez <[EMAIL PROTECTED]> wrote:
Thanks Tsjerk,
you 're right. But are there any form to eliminated this water that it
isn't by hand or solvate only in the z axes ? There are a lot of
water molecules between the monolayer in my system.
Thanks again.
Maite.
On 3/14/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Maite,
>
> After removing water molecules, you forgot to change the number of
> atoms listed in the second line of the file. Editconf expected more
> atoms to come, but ran into the box (the line you see in the error).
> Try to get a bit familiar with the file formats of Gromacs. That can
> often help to solve problems.
>
> Best,
>
> Tsjerk
>
> On 3/14/07, maite lopez <[EMAIL PROTECTED]> wrote:
> > Hi:
> > I am working on peptide-membrane simulation under lipid (DPPC, from
> > Peter Tieleman group site). I've solvated the system using the x and y
> > vectors of the initial box (membrane box), but i increased the vector
> > in the z axes . I've
> > eliminated the water molecules that are interacting with the apolar coils
of the
> > lipids, but when i try to reorder the atoms with the editconfig command it
gives
> > this error :
> > Fatal error:
> > Invalid line in peptide_dppc64_water.gro for atom 20704:
> > 4.72500 4.23200 12.00000
> >
> > this is a water atom. I eliminated this water molecule and the same
> > error comes. The line format is ok.
> >
> > If i eliminated in the initial .gro only a water molecule that it is
> > interacting with
> > lipids the same happen.
> >
> > i visualizated the system and these atoms aren't in contact.
> >
> > I've done the last steps because when i run a MD of the unmodified system,
> > the water molecules that are interacting with the apolar coils of the
> > lipids form clusters between the monolayers.
> >
> > How can i eliminate this molecules or solvate the system only in the z axes?
> >
> > I want to add more water molecules and to equilibrated other membranes
> > of this site, but i'll always obtain water molecules between the
> > monolayers.
> >
> > Any help will be highly appreciated.
> >
> > Maite
> > _______________________________________________
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list [email protected]
> http://www.gromacs.org/mailman/listinfo/gmx-users
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_______________________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
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