[gmx-users] trjconv error

[Rama Krishna Koppisetti]

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


thanks





On Thu, Nov 21, 2013 at 4:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Thu, Nov 21, 2013 at 5:50 PM, Rama <ramkishna72 at gmail.com> wrote:
>
> > Hi
> >
> > After MD run, lipids are broken at the boundaries. I'm trying to fix
> > trajectory by following command
> >
> > trjconv -f a.trr -o a1.trr -s b.tpr -pbc mol
> >
> > then I use a1.trr file(output file from above command) to make snapshots
> by
> > following command:
> >
> > trjconv -s b.tpr -f a1.trr -o c.gro -skip 5 -sep
> >
> > it shows some fatal error:
> > Fatal error:
> > Index[8271] 8272 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.
> >
> >
> You haven't shown what group you are choosing for output in the first
> invocation of trjconv, but it is fairly clear that you  are not saving all
> the necessary coordinates.
>
> -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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