[gmx-users] trjconv error

Rama Krishna Koppisetti ramkishna72 at gmail.com
Fri Nov 22 02:43:07 CET 2013


Thanks Justin ,

I'll continue by keeping all atoms in the next step.

*--RK*


On Thu, Nov 21, 2013 at 7:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
>
> --
>
> ==========================================
>
> 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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