[gmx-users] trjorder problems

[Mark Abraham]

cfgauna at lab.cricyt.edu.ar wrote:
> Hi all:
> I am trying to know how many and which molecules of solvent are near my
> system, I read the manual and I found that one can do this using trjorder,
> but   I can not do this with my Gromacs version 3.3.2 beacause in this
> version there is a problem and one can not use options -o and -r together.
> I also tried with version 3.1.4 but option -r is not available.  If I do
> not use -r option the output file .pdb is very large (30Gb) and I can not
> read it!
> Can any one please give any suggestion?

You don't have to use every frame of the trajectory. Read "trjorder -h" 
and consider using the -b, -e, -dt flags.

Mark