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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 5 13:39:40 CEST 2015

Hi Pavan,

Please don't reply to a digest, at least not without editing the subject.

And remove everything that is not relatsd to what you're replying to.

Maybe the answer was what you were looking for, but you expected it in a
different form. The distance from a given reference position is easily
obtained from the coordinates of the particle. Hence the suggestion to use
gmx traj.

g_msd should also do the trick.



On Aug 5, 2015 13:10, "PAVAN PAYGHAN" <pavanapex at gmail.com> wrote:

Dear Tsjerk,

Thanks a lot for your reply. It was really helpful.
However it does not answer what I am looking for.
1. I want to calculate changes in the form of distance along the entire
trajectory as if I am fitting all the frames and then calculating the
changes for the same atom (or residue).
2. As I am checking the distance changes for same atom (or residue) is
there any way I can answer this using gromacs tools or any other method in
your knowledge?

Thanks a lot in Advance,

Pavan Payghan

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