[gmx-users] trjorder Problem!!

[ankur gupta]

Dear Gromacs Users,
I have dissolved my 47 residue protein in around 10000 water molecules and
now want to know the diffusion coefficient of water near and far away from
the protein.But while running the trjorder I have given the command
trjorder -f xyx.trr -s xyz.tpr -da n -o output.trr
where n is any integer
Everytime I am getting this error
Fatal error: The reference atom can not be larger than the number of atoms
in a molecule
I have tried with all the integer n but everytime the same error.Please
tell me why is it so??
is there any other way out??
Also I am new in this field so please give me some reference/tutorial
where I can know how far from the protein we should take the water
molecule to calculate the diffusion coefficient, and other basic stuff
regarding protein water interface.

Thanking you
Sincerely
Ankur


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