[gmx-users] trjorder time-consuming

[Justin Lemkul]

On 6/3/15 8:52 AM, Rebeca García Fandiño wrote:
> Dear GROMACS users,
> I am using the command "gmx trjorder" with a single frame of a trajectory, to order the water molecules according to the smallest distance to a molecule. The system is very small (4400 atoms), however gmx trjorder is taking more than 1 hour to finish!! Is it normal to be so time-consuming using only a single frame or maybe is there anything wrong with the execution?
>

No, that's not normal.  Trajectories should finish in less time.

> gmx trjorder -f frame.pdb -s topology.tpr -o frame_ordered.pdb -da 0 -na 3
>

Does -da 1 make a difference?  I wouldn't imagine COM vs. O position would 
substantially change the outcome, and you avoid having to calculate the COM for 
every molecule with -da 1.

-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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