[gmx-users] mismatch atoms?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 29 09:02:36 CEST 2012

On 29/08/2012 4:22 PM, Albert wrote:
> Dear:
>   I am trying to extract one frame of my simulation results by commands:
> trjconv -f md.trr -s tuned.tpr -o md.xtc -pbc mol -timestep 100 -n 
> out.ndx
> trjconv -f md.xtc -s tuned.tpr -fit rot+trans -o out.pdb -dump 
> 133000.000 -n out.ndx
> However, it said:
> Fatal error:
> Index[31715] 31716 is larger than the number of atoms in the
> trajectory file (31715). 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 
> website at http://www.gromacs.org/Documentation/Errors
> Does anybody has any advices?

The error means exactly what it says. You need to think about what's in 
those files and why a mismatch is occurring, e.g. you used xtc output 
groups smaller than System.


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