[gmx-users] need help !

[electronsource at free.fr]

Hi

Thanks you for your help .The analyses of my MD work perfectly. 

----- Mail original -----
De: "Mark Abraham" <mark.j.abraham at gmail.com>
À: gmx-users at gromacs.org
Envoyé: Jeudi 9 Mars 2017 17:07:07
Objet: Re: [gmx-users] need help !

Hi,

See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Thu, Mar 9, 2017 at 5:04 PM <electronsource at free.fr> wrote:

> 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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