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

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 2 19:21:51 CET 2011

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.


> 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?


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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