Hi Pavan, The distance from an atom to itself is zero by definition. Also, distance in only defined between things, so, indeed, you need two groups for gmx dist. If you mean distance over PBC it's a different matter. Then you want the distance between a group and any of its periodic images. That's what gmx mindist is for. If it's the position you need, then you want gmx traj.
Hope it helps, Tsjerk On Aug 5, 2015 08:34, "PAVAN PAYGHAN" <pavana...@gmail.com> wrote: > Dear Groamcs Users, > > I am in need to calculate distance changes for a single atom (same atom) > along the simulation time. > I tried to do so using g_dist by giving input of same atom index group > twice for the calculation, output was in null values, which can not be > true. > To my surprise g_dist needs two different groups in order to calculate > distance vs Time changes. > Is there any tool or method available in gromacs for doing such > calculation?? > > Thanks in advance, > -- > 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.
