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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 5 09:22:14 CEST 2015

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,

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,
> --
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