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.
Don't.
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.
Mark
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