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

[Justin A. Lemkul]

leila karami wrote:
> 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.

This is not what Chris told you.  Please read his message(s) more carefully. 
You've been advised to re-install Gromacs in a different location (not the 
default /usr/local/gromacs) to avoid confusing the files.  Chris did not say 
that there is any different directory structure.

It would also be useful if you post the Makefile you're using.  This is a fairly 
straightforward task, so if it's failing, something is fundamentally wrong with 
what you're doing, but you haven't provided the proper details yet.

-Justin

> 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?

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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