[gmx-users] calculating single atom changes along the trajectory as a measure of distance

[Michael Cristòfol Clough]

Hello Pavan,

If I understand correctly you might want to use root mean square deviation
(g_rms) and specifying only the atom of interest.

Michael





On 5 August 2015 at 09:22, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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" <pavanapex at 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-request at 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-request at gromacs.org.
>