[gmx-users] calculating single atom changes along the trajectory as a measure of distance
Michael Cristòfol Clough
michaelcristofol at gmail.com
Wed Aug 5 13:27:12 CEST 2015
If I understand correctly you might want to use root mean square deviation
(g_rms) and specifying only the atom of interest.
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,
> 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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