[gmx-users] trjorder Problem!!

[Osmair Vital de Oliveira]

On Fri, 27 Feb 2004, ankur gupta wrote:

> 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

-na n is number of atoms in a solvent molecule
-da m is atom used for the distance calculation (m =< n)
 eg., water (solvent): -na 3 and -da 1 or 2 or 3

> 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
>
>
> "You are making progress if each mistake You make is a new one"
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Osmair
Brazil