[gmx-users] genbox peptide-membrane simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 2 11:06:27 CET 2007


The option -d sets a distance to be met on all sides, considering all
the atoms to in the ouput selection. That's not what you want for a
membrane now, is it? So, you don't want that option. You should have a
box from the lipids anyway, I guess (used to equilibrate that system),
just extend the z-coordinate (third number in the last row of the .gro
file) such that your peptide fits in.

Furthermore, molecules can't go out of the box, there is no outside!
There's only wrapping from one side to the opposite one. Please read
the manual and the mailing list regarding periodic boundary conditions
(and setting up membrane-peptide simulations).


On 2/2/07, maite lopez <lopezmai at gmail.com> wrote:
> Hi gromacs users:
> I'm simulating a peptide-dppc64 system. When i create my box with
> editconf program  (editconf -f input.gro -o output.gro  -bt triclinic
> -c -d 1.5) and i solvate, the molecule go out of the box. I used many
> kind of box and some  box sizes.
> My system size is 4.936 4.408 and 10.503 nm. Should i use -d option
> with editconf? I've found in the gmx-users list and in many tutorials,
> it should be no less than 0.5.
> I don't want to solvate the system in x and y axes due to the
> interaction betwen lipids and water. I did it whit editconf -f
> input.gro -o output.gro  -bt triclinic  -c  -box 4.936 4.408 12 , but
> i didn't use the -d option. Is that ok?
> So my question is: Can I do something whit -d and -box option of
> editconf program for resulting in a system that it doesn't solvate in
> x and y axes, and the molecule isn't out? I need to solvate in z axes.
> whould you please help me?
> best regard
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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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