[gmx-users] need help !

[electronsource at free.fr]

Hello.

I am new on using gromacs and i have problems with my files .I need to remove water and ions from an .xtc in order to keep my RNA.Then i have to center the system in the box and remove some frame to be able to visualize it.

Here are the commands lines that i use:

trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx

i chose only RNA
 
trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n index.ndx

then i convert it into pdb and i remove some frame 

trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb 


I have a few question :

is my code right ?

what do we use index files ?

How can i be sure that i have a good .tpr file because sometimes i have errors.

Tahnks you !!