# Single-stranded dna rmsd analysis **URL:** \ **Category:** User discussions\ **Created:** [June 16, 2022, 1:54pm UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309 "2022-06-16T13:54:45Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [June 16, 2022, 1:54pm UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309/1 "2022-06-16T13:54:45Z")
GROMACS version:2020 GROMACS modification: Yes Hi,I applied md simulation using amber force field which is OL15,on my single-stranded apo form DNA structures.for analysis I get confused .in order to rmsd analysis,I created index file each of residues (DC,DT,DA,DG) and added new groups for selection. selection group for least squares fit I chose DA residues ,select group for Rmsd calculation System BUT the graph is ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8296104d360db0a5d3da0c39ab62ecaf7d468fe7.png) selection group for least squares fit I chose system residues ,select group for Rmsd calculation DA, The graph is ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/4840918bafd7b6194c03ecaf3ad3fdee58ba3440.png) Could you help me which graph I can prefer or which groups I can choose ? could anybody explain me ? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 16, 2022, 2:06pm UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309/2 "2022-06-16T14:06:17Z")
Neither. You should not fit or calculate with System, because that just gives you results that are washed out by the solvent (which is what appears to be the case in the first plot). ---
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [June 16, 2022, 5:27pm UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309/3 "2022-06-16T17:27:11Z")
Thank you,so two graphs are not correct ![Screenshot from 2022-06-16 20-16-18](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/592b883edab4903293361ff166c481aec84d1783.png) into the picture shows that my groups,so in order to rmsd calculation for DC or any groups how to do selection.Could you guide me please ---
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [June 17, 2022, 7:55am UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309/4 "2022-06-17T07:55:23Z")
I created backbone groups . ![Screenshot from 2022-06-17 10-44-54](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8eb843ad1f4aec87d61c349c7130dd0f59312aa8.png) when I chose firstly backbone,secondy system The graph is ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0a1c3b59b5c9b687735782c4d7e0d07525f66124.png) When I chose firstly system,secondly backbone .The graph is : ![rmsd1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0bcb397ba3b449463d1879f067aada7518d1a218.png) What is my fault,what is the difference between two graphs ,which graph is true for me ,could anybody explain and suggest to me,I will be very grateful.Thank you ---
**Author:** ![sibasankar.p](https://avatars.discourse-cdn.com/v4/letter/s/b9e5f3/32.png) [@sibasankar.p](https://gromacs.bioexcel.eu/u/sibasankar.p)\ **Post date:** [September 27, 2022, 6:57am UTC](https://gromacs.bioexcel.eu/t/single-stranded-dna-rmsd-analysis/4309/5 "2022-09-27T06:57:11Z")
Use the same selection from the reference structure that you are fitting for RMSD. While calculating for backbone, exclude hydrogen atoms. You can add one more extension to your command -fit rot+tans. It seems you system is not equilibrated properly. Try to extend the run.