[gmx-users] Water out of box? Negative Z-Coordinates

[Justin Lemkul]

On 3/31/14, 5:39 PM, GtrAngus wrote:
> Hi :)
>
> I am having a little problem with my cubic box full of water. I am trying to
> calculate the polarization density so I divide the box into different layers
> in Z-direction and do my calculation for every layer. The box goes from 0 nm
> to 4 nm in every direction. Now I realized that some of my atoms were not
> taken into consideration because they have negative Z-coordinates! How do I
> have to change the PBC to avoid this problem? :)
>

Well, what did you do to observe negative coordinates?  In principle, all unit 
cells in Gromacs have an origin at (0,0,0) and the way mdrun works you should 
only get positive coordinates, IIRC.  So the emergence of negative coordinates 
is a bit odd, but there's nothing wrong with it.

> Does a negative value of e.g. -0.1 mean the atom has the position 3.9 in
> reality? If that's true then I can fix this myself with my C-Code.
>

Yes, assuming your box dimensions are invariant (i.e. NVT/NVE), but trjconv 
should handle this so you don't have to reinvent the wheel.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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