Hi, On Thu, Mar 9, 2017 at 3:11 PM <electronsou...@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 !! > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.