# H-Bond distance **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [January 5, 2022, 11:25am UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402 "2022-01-05T11:25:35Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Akki](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/akki/32/958_2.png) [@Akki](https://gromacs.bioexcel.eu/u/Akki)\ **Post date:** [January 5, 2022, 11:25am UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/1 "2022-01-05T11:25:35Z")
Can anyone please help me on how to choose hydrogens for calculating H-Bond distance in a particular protein… When I am visualizing my protein in pymol, unable to figure out, which hydrogens are interacting with each other… Please help me on how to choose hydrogens and make index file so that I can calculate distance between then using **gmx distance** command ---
**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\ **Post date:** [January 5, 2022, 5:24pm UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/2 "2022-01-05T17:24:27Z")
Gromacs automatically classifies atoms according to which are hydrogen bond donors and acceptors. You can read it here: [gmx hbond — GROMACS 2019 documentation](https://manual.gromacs.org/documentation/2019/onlinehelp/gmx-hbond.html) " OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using `-nitacc` ." You can check the distance by using `-dist` option. for example gmx hbond -f name\_of\_xtc\_trajectory\_file.xtc -s name\_of\_tpr\_file.tpr -dist hbond\_distance.xvg If you want to check the distance between specific groups, you need to create an index file in advance, check here how to do it [gmx make\_ndx — GROMACS 2019 documentation](https://manual.gromacs.org/documentation/2019/onlinehelp/gmx-make_ndx.html) or here you have an example [KALP-15 in DPPC](http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html) and you add index file in gmx hbond command: gmx hbond -f name\_of\_xtc\_trajectory\_file.xtc -s name\_of\_tpr\_file.tpr -n your\_index\_file.ndx -dist hbond\_distance.xvg I don’t know is it possible in Pymol to show where hydrogen bonds are. You can check the distance and angle. Here is [Hydrogen bonds — GROMACS 2021.4 documentation](https://manual.gromacs.org/documentation/current/reference-manual/analysis/hydrogen-bonds.html) hydrogen bond criteria, I use mostly default distance between acceptor (A) and Donor (D) is 0.35 nm or lower and H-D-A angle 35 degree or lower ---
**Author:** ![Akki](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/akki/32/958_2.png) [@Akki](https://gromacs.bioexcel.eu/u/Akki)\ **Post date:** [January 5, 2022, 5:45pm UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/3 "2022-01-05T17:45:04Z")
Thank you sooo much for explaining… I will try to apply it… ---
**Author:** ![Akki](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/akki/32/958_2.png) [@Akki](https://gromacs.bioexcel.eu/u/Akki)\ **Post date:** [January 7, 2022, 12:00pm UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/4 "2022-01-07T12:00:18Z")
Can you please help me on how to plot graph between H-bond distance and number of frames. Just like the one I am attaching here: ![Screenshot 2022-01-07 172528](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0d8fd8622a06a3c9af2afcd5d8bd27321d3c8e4d.jpeg) ---
**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:** [January 7, 2022, 1:10pm UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/5 "2022-01-07T13:10:08Z")
You can calculate the distance between any pair of atoms (or any groups of atoms) with `gmx distance`. ---
**Author:** ![Akki](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/akki/32/958_2.png) [@Akki](https://gromacs.bioexcel.eu/u/Akki)\ **Post date:** [January 9, 2022, 10:04am UTC](https://gromacs.bioexcel.eu/t/h-bond-distance/3402/6 "2022-01-09T10:04:13Z")
okk sir… i will try to do it…