[gmx-users] trjconv error

[Justin Lemkul]

On Thu, Nov 21, 2013 at 8:17 PM, Rama Krishna Koppisetti <
ramkishna72 at gmail.com> wrote:

> Hi Justin,
>
> the groups that I selected in first invocation was:
>
> Group    22 (          Water) has 28857 elements
> Group    23 (            SOL) has 28857 elements
> Group    24 (      non-Water) has  8271 elements
> Group    25 ( Water_and_ions) has 28870 elements
> Select a group: 24
> Selected 24: 'non-Water'
> trn version: GMX_trn_file (single precision)
> Last frame       1500 time 15000.000    ->  frame   1500 time 15000.000
>
> then for second command I selected the same group
>
> Group    22 (          Water) has 28857 elements
> Group    23 (            SOL) has 28857 elements
> Group    24 (      non-Water) has  8271 elements
> Group    25 ( Water_and_ions) has 28870 elements
> Select a group: 24
> Selected 24: 'non-Water'
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> Setting output precision to 0.001 (nm)
>
> -------------------------------------------------------
> Program g_trjconv, VERSION 4.5.5
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c, line: 1166
>
> Fatal error:
> Index[8263] 37121 is larger than the number of atoms in the
> trajectory file (8271). 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
>
>
Right, so there are more atoms in the .tpr file than the .trr, hence the
mismatch when trying to read in a .trr frame - it doesn't match the .tpr.
Rule of thumb - keep all the atoms until the very last step unless you want
to do more work creating different .tpr files.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
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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