[gmx-users] trjorder Problem!!

Xavier Periole x.periole at chem.rug.nl
Fri Feb 27 13:44:00 CET 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
>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??
n seems to be (in your case) the atom number of the water molecule that will
be used to calculate the distance to the protein. So it must not be more 
than 3
as the water molecule got 3 atoms. Keep it at one seems to be the best 

>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


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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