Hi, See also http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
Mark On Thu, Mar 9, 2017 at 5:04 PM <electronsou...@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.abra...@gmail.com> > À: gmx-us...@gromacs.org, "gromacs org gmx-users" < > gromacs.org_gmx-users@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 <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. > -- > 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.