[gmx-users] genbox + editconf

[Anton Feenstra]

Senthil Kandasamy wrote:
> 
[...]
> I decided to try genbox on a pre-existing lipid bilayer, just as a test
> case. If I do things correctly, i should get a lipid bilayer with extra
> waters inserted, especially between the leaflets.Though not physically
> valid,it would be an easy way to check things.

Right.

[...]
> But Solvated.gro is not what it should be. I have my original bilayer
> still centered at the origin. Then,there is this additional rarified
> water box (the new added waters ) that is not centered at the origin. It
> seems to be translated by half the box length in all three directions so
> that there is only one common octant between the original bilayer and my
> new added waters. Almost seems like the water box was not centered at
> the origin to begin with and the origin is at one of the corners of the
> box.(though it definitely was and I confirmed it by repeating these
> steps multiple times.)
> 
> The box size in my solvated.gro is still 10 x 10 x 10, while the system
> size is now ~15 x 15 x 15.
> 
> I am obviously doing something wrong here. Is there some option that I
> am leaving out? Can some body help me out here?

This is a virtual error. If you would apply the periodicity here, both
parts of the system (the bilayer + water box and the 'new' water box)
will overlap nicely. genbox will not touch your 'solute' (-cp) coordinates,
(so the bilayer stays where it was, on the origin), but it builds from
your periodic water box (-cs) a new water 'block', which will be centered 
inside the box.

I don't actually see why you would want to center your system on the 
origin before using genbox. The convention in Gromacs is to have the 
system centered in the box *and* also to have all molecules whole. 
So, your two 'editconf -center -pbc' steps seem obsolete to me.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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