[gmx-users] regarding trjconv

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 17 16:10:55 CEST 2008

Anamika Awasthi wrote:
> Dear all,
>             RMSD and RMSF of my protein is showing abnormal 
> flucutuation. To overcome this problem I am using following commands-->
>           trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole
>           trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump
>                but this second command is showing fatal error:
>               Index[35] 334 is larger than the number of atoms in the 
> trajectory file (330)
>  pls help me to understand this and to sort out this problem.

That last command shouldn't involve index groups at all. Since it also 
break more catastrophically with a space in the filename, I'm guessing 
you've reconstructed what you thought you gave as a command.


Computers are literal, and so you should be cutting and pasting your 
exact input and output. Making us guess wastes everybody's time.

Probably you used an -s flag, and the index group you chose is larger 
than the size of the atom set in your trajectory. Compare the contents 
of xtc-groups in your .mdp file with this group you chose with trjconv.


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