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

[Justin Lemkul]

On 3/31/14, 7:12 PM, Justin Lemkul wrote:
>
>
> 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?
>

Amendment: you need to provide a .tpr if you want trjconv to do anything useful. 
  The trajectory has no knowledge of what defines periodicity.

-Justin

-- 
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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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