[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

[leila karami]

Dear Chris

very thanks for your time and attention.

only difference between what you said and what I did is in the
location of template directory:

for me >>>>>>>>>>>> gromacs-4.0.7/share/template
for you >>>>>>>>>>>> gromacs-4.0.7/exec/share/gromacs/template

in my gromacs there is not exec directory even in fresh and original
version of gromacs4.0.7. I did rest of the steps exactly as you said.
what is your mean of  (Did you do the compilation of gromacs)? make -f
Makefile.my_tool? Yes I did.

I will test all of steps on fresh version of gromacs4.0.7. I hope that
solve my problem. after (download a fresh version of gromacs4.0.7,
name it with a special
directory, make the modification directly to the *original* trjconv,
and compile it. Now you will have a special version of trjconv.) I
should install gromacs. is it true?