[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Justin Lemkul]

On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote:
> Hi all,
> I am running a simulation and I find that the output coordinates of the simulation stored in “final_coordinates.gro” are distinctively different to any of the frames from “trajectory.gro” which I obtain from :
> 
> trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro
> 
> When I visualise final_coordinates.gro they look wrong, when I visualise trajectory.gro frame by frame it looks correct.
> 
> How can this be possible? Is it a common problem?
> 

Please define what "wrong" and "correct" mean.  The raw trajectory from mdrun 
does not have PBC-corrected frames, so things may be broken.  If you're done 
reimaging with trjconv, you've changed the representation.  You can dump the 
final coordinates from the .xtc, make molecules whole, and these should match 
the final configuration written 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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