# How do we use gmx polystat? **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [April 26, 2024, 11:24am UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997 "2024-04-26T11:24:59Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [April 26, 2024, 11:25am UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997/1 "2024-04-26T11:25:00Z")
Hi All, My system contains 60 polymers and I want to calculate the average end-to-end distance change with time. In the index file if I define indexes of the starting end and the ending end of the polymer with the following command would it give me the average end-to-end distance with time? gmx polystat -s …/…/…/run.tpr -f run0-14\_nopbc.xtc -o 0.xvg -n index.ndx My index file looks as follows. For each line, it contains indexes for the starting end and end atom index [poly60] 6 149 164 307 322 465 480 623 638 781 796 939 954 1097 1112 1255 1270 1413 1428 1571 1586 1729 1744 1887 1902 2045 2060 2203 2218 2361 2376 2519 2534 2677 2692 2835 2850 2993 3008 3151 3166 3309 3324 3467 3482 3625 3640 3783 3798 3941 3956 4099 4114 4257 4272 4415 4430 4573 4588 4731 4746 4889 4904 5047 5062 5205 5220 5363 5378 5521 5536 5679 5694 5837 5852 5995 … ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [April 26, 2024, 2:42pm UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997/2 "2024-04-26T14:42:26Z")
That should work. Have you tried? ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [April 26, 2024, 3:20pm UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997/3 "2024-04-26T15:20:43Z")
@hess Yes, I tried. However, I was unsure whether I needed to provide all indexes (all atoms) in the index file. That way too, I can get values and have doubts about which way is correct. Thank you for clearing my doubts. So now I know that I need to provide only the indexes of the two ends to get the correct end-to-end distance of the polymer. ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [December 1, 2025, 8:47pm UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997/4 "2025-12-01T20:47:44Z")
@hess Hi again, Since we defined only two atoms in the index file, is the radius of gyration calculated using only those two specified atoms, or does the code include all atom indices between the first and second values listed in each line of the `[poly6]` group? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 2, 2025, 7:12am UTC](https://gromacs.bioexcel.eu/t/how-do-we-use-gmx-polystat/8997/5 "2025-12-02T07:12:28Z")
The idea is to supply an index group that contains all atoms of all molecules you want to analyze. The end to end distance is taken between the first and last atom from each molecule in this index group.