[gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 6:17 PM, Alex wrote:
> Hi all,
>
> I've got a system that includes a group named "CNT" consisting of 2837
> atoms. To save space, I am outputting (at a very high rate) a compressed
> trajectory that contains only that group. The GMX version is 5.0.5. Here's
> the relevant mdp excerpt:
>
>
> nstxout             =  10000
> nstcomm             =  1000
> nstxout-compressed  =  10
> compressed-x-grps   =  CNT
> nstvout             =  1000
> nstfout             =  500
> nstlog              =  100
> nstenergy           =  500
> nstlist             =  20
>
> Upon trying to convert the compressed trajectory, after selecting the
> appropriate group from the menu (CNT, 2837 atoms), I get:
>
> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>
> output:
> -------------------------------------------------------
> Program trjconv, VERSION 5.0.5
> Source code file:
> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
> line: 1330
>
> Fatal error:
> Index[2645] 2838 is larger than the number of atoms in the
> trajectory file (2837). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Where's this single-atom discrepancy coming from? Any suggestions?
>

Whatever you selected as output contains more atoms than are in the trajectory. 
  Note that it's not necessarily a single-atom discrepancy, it's just that the 
fatal error is triggered as soon as an index that is out of range is identified. 
  You're only outputting CNT, and presumably the .tpr contains more atoms, so 
the selection you're making can only be CNT or some subset of those atoms.

-Justin

-- 
==================================================

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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