[gmx-users] g_covar warnings

Justin Lemkul jalemkul at vt.edu
Thu Mar 27 18:34:22 CET 2014

On 3/27/14, 1:27 PM, João Henriques wrote:
> Hello everyone,
> The documentation reads:
> """
> All structures are fitted to the structure in the structure file. When this
> is not a run input file periodicity will not be taken into account.
> """
> This is rather cryptic, what does it mean in practice? No tpr, no party?
> What if I use a properly centered and whole .gro file?
> When ran with a .gro as the structure input file, I get two warnings. One
> is related to the masses, which are non-existent in the .gro, but I don't
> need them anyway. The second warning is honestly confusing me even more.
> """
> WARNING: If there are molecules in the input trajectory file
>           that are broken across periodic boundaries, they
>           cannot be made whole (or treated as whole) without
>           you providing a run input file.
> """
> The documentation points out to the structure input file and now it's the
> trajectory? What's going on? Do I also need to make each frame whole in the
> input .xtc? Can someone elaborate on this?

The documentation consistently refers to the run input file.  A .tpr has record 
of how periodicity is treated.  Nothing else does.  If you don't tell g_covar 
(like most Gromacs tools) how periodicity is treated, you can get garbage as a 
result.  The trajectory may have "broken" molecules, because mdrun doesn't care 
how they look - it has a run input file and thus knowledge of periodicity.  When 
running analysis like g_covar, if the bonded connectivity of the molecule and 
the periodicity are unknown (again, if you're not using a .tpr), then absolute 
displacements of coordinates are used, thus your analysis might be totally hosed 
if the molecule "splits" - that would be a rather dramatic structure change 
detected by g_covar.  In fact, so dramatic that it's false.



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


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