[gmx-users] peptide-membrane simulations

[Tsjerk Wassenaar]

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 <lopezmai at gmail.com> 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 <tsjerkw at gmail.com> 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 <lopezmai at gmail.com> 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
> > _______________________________________________
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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