[gmx-users] peptide-membrane simulations

[Tsjerk Wassenaar]

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