[gmx-users] Getting error using gmx trjconv

Saikat Pal saikatpaliitg at yahoo.com
Mon Oct 8 15:51:23 CEST 2018

Dear all,I am getting this kind of error :

Command line:
  gmx trjconv -s 148d-wat-0-reduce-oct_GMX-1.gro -f b.tng -o c.tng -fit rot+trans -n test-o.ndx

Will write tng: Trajectory file (tng format)

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

WARNING: If there are molecules in the input trajectory file
         that are broken across periodic boundaries, they
         cannot be made whole (or treated as whole) without
         you providing a run input file.

Select group for least squares fit
Group     0 (            URE) has  4000 elements
There is one group in the index
Select group for output
Group     0 (            URE) has  4000 elements
There is one group in the index
Reading frame       0 time 1035500.000   
Precision of b.tng is 0.001 (nm)

Program:     gmx trjconv, version 2018.3
Source file: src/gromacs/gmxana/gmx_trjconv.cpp (line 1350)

Fatal error:
Index[3498] 4001 is larger than the number of atoms in the
trajectory file (4000). There is a mismatch in the contents
of your -f, -s and/or -n files.

Thanks and Regards,
Saikat Pal

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