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

[Justin Lemkul]

On 3/31/14, 7:01 PM, GtrAngus wrote:
> OK, just in case I just want the atoms in the box and I don't care about
> Molecules, this should work?
>
>> trjconv -f traj.trr -o traconv.trr -pbc atom
>
> Because I tried and it does SOMETHING. Some atoms are in the box now (I
> guess) but still atoms are out of the box. Do I have to add some commands?

That observation conflicts with the very definition of what -pbc atom does.  How 
large is the box?  Do you have correct vectors in the trajectory?  I still don't 
know why mdrun produced negative coordinates in the first place - the run was 
done with mdrun, correct?

> Or do I have to repeat this command several times?
>

Repetition of the same thing will produce nothing useful.

> -pbc mol or -pbc whole didn't do a better job at all :( The problem stays
> the same here.
>

I really don't understand why that is.  Any of the above should ensure that all 
coordinates are > 0.

-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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