[gmx-users] need help !

[electronsource at free.fr]

Thank you for yours answers .

I'm a felling more comfortable.So to sum up my index file is filled with the coordonate that i care.
So in my case if i want only the RNA i just have to delete all the others data.And when i run my .xtc for make it shorter il 'll have only water 
Or i have just to choose the RNA in the menu after using trjconv 

  

----- Mail original -----
De: "Mark Abraham" <mark.j.abraham at gmail.com>
À: gmx-users at gromacs.org, "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Envoyé: Jeudi 9 Mars 2017 16:30:36
Objet: Re: [gmx-users] need help !

Hi,

On Thu, Mar 9, 2017 at 3:11 PM <electronsource at free.fr> wrote:

> 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 ?
>

Seems plausible.

what do we use index files ?
>

To specify the indices of subsets of atoms that are of interest.


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

If it ran your simulation, it's good.

Mark


> Tahnks you !!
>
>
>
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