[gmx-users] How to determine box shape and parameters from a run

[Justin Lemkul]

On 11/3/15 5:56 AM, Ramon Crehuet wrote:
> Dear all,
> This is a very simple question, but I could not find the answer in the
> documentation. Some time ago I run a simulation and now I don't remember the box
> shape and sizes I used. In which file is this information contained?
> A related question is whether the box volume is printed somewhere or I need to
> calculate it from the parameters.
> Thanks in advance,
> Ramon
>
> PS. My log contains Box-X Box-Y and Box-Z parameters. Does that mean I used a
> rectangular box?
>

Box vectors are stored in the .edr file, and you can verify the shape from the 
vectors printed to any coordinate file (your starting coordinates, dumped from 
the .tpr if needed, or any final coordinate file printed by mdrun).

-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 629
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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