[gmx-users] membed error

Justin Lemkul jalemkul at vt.edu
Thu Oct 15 16:47:22 CEST 2015

On 10/15/15 10:44 AM, badamkhatan togoldor wrote:
> Dear GMX userI got following error on the membeding process.Then i have to change my box type in here?
>   and also XTC error : I have to run it more bigger machine?
> Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
>           Box (3x3):
>              Box[    0]={        -nan,         -nan,         -nan}
>              Box[    1]={        -nan,         -nan,         -nan}
>              Box[    2]={        -nan,         -nan,         -nan}
>           Can not fix pbc.
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1
> Source code file: /local/cache/mhhakala/gromacs-5.1/src/gromacs/fileio/mdoutf.c, line: 364
> Fatal error:
> XTC error - maybe you are out of disk space?

More likely mdrun is trying too write some nonsensically large value to some 
coordinates and triggering the error.  Note that -nan above means "not a 
number," so the box has collapsed completely.  Sounds like the process simply 
failed, but there's nothing diagnostically useful here.



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


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