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

[Justin Lemkul]

On 3/31/14, 6:12 PM, GtrAngus wrote:
> Justin Lemkul wrote
>> 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.
>
>
> I faced the problem while I made a sum over all dipolmoments. Every time I
> calculated it, the counter goes ++. The number varies for every loop so I
> made a if-loop with if(pos[i][ZZ] < 0) and a new counter counts the atoms
> with a negative Z-coordinate.
>
>
>
> Justin Lemkul wrote
>> 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.
>
> Yes, it is NVT. I looks like you are familiar to trjconv ! :) I looked it up
> in the manual. Is this syntax correct for my problem?
>
>> trjconv -f traj.trr -pbc atom
>
> Or which one would you prefer?
>

You'll need whole molecules, otherwise your dipole moments will be junk.  Using 
-pbc atom will put all the atoms in the box but will not guarantee they are 
intact.  Probably -pbc mol or -pbc whole after -pbc atom would be better.

-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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