# GMX Trajectory not extracting force or velocities **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [November 5, 2021, 5:44pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087 "2021-11-05T17:44:37Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![organicchemistry\_01](https://avatars.discourse-cdn.com/v4/letter/o/6bbea6/32.png) [@organicchemistry\_01](https://gromacs.bioexcel.eu/u/organicchemistry_01)\ **Post date:** [November 5, 2021, 5:44pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/1 "2021-11-05T17:44:37Z")
GROMACS version: 2021.3 GROMACS modification: Yes I have these enabled in my `md file`: ```auto nstxout = 500 nstvout = 500 nstfout = 500 ``` but when I use: ```auto gmx trajectory ``` I could only extract the position but not the velocities and forces. How to extract forces and velocities from my trajectory files? ---
**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:** [November 6, 2021, 4:51pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/2 "2021-11-06T16:51:37Z")
What does `gmx check` tell you about the contents of the trajectory? What was your exact `gmx trajectory` command? ---
**Author:** ![organicchemistry\_01](https://avatars.discourse-cdn.com/v4/letter/o/6bbea6/32.png) [@organicchemistry\_01](https://gromacs.bioexcel.eu/u/organicchemistry_01)\ **Post date:** [November 16, 2021, 12:40pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/3 "2021-11-16T12:40:35Z")
This is what appears after: `gmx check -f md.trr -rmsd` ```auto Item #frames Timestep (ps) Step 50001 1 Time 50001 1 Lambda 50001 1 Coords 50001 1 Velocities 50001 1 Forces 50001 1 Box 50001 1 ``` ---
**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:** [November 16, 2021, 8:47pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/4 "2021-11-16T20:47:07Z")
And what was your `gmx trajectory` command? ---
**Author:** ![ABaer](https://avatars.discourse-cdn.com/v4/letter/a/71c47a/32.png) [@ABaer](https://gromacs.bioexcel.eu/u/ABaer)\ **Post date:** [April 21, 2022, 12:51pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/5 "2022-04-21T12:51:21Z")
Hi all, I have in principle the same problem: I would like to extract the molecular COM velocity for a subgroup (“LIG”) of the system with the following command: `gmx trajectory -f trajectory.trr -s topol.tpr -e 100 -ov vel_tmp.xvg -seltype mol_com -select LIG` This will result in an empty velocity file (`vel_tmp.xvg`), which only contains the `.xvg` header. If I also want to extract the position with the following command: `gmx trajectory -f trajectory.trr -s topol.tpr -e 100 -ox pos_tmp.xvg -ov vel_tmp.xvg -seltype mol_com -select LIG` I will obtain the following error message: ```nohighlight ------------------------------------------------------- Program: gmx trajectory, version 2021.3 Source file: src/gromacs/analysisdata/datastorage.cpp (line 828) Function: gmx::AnalysisDataStorageFrame& gmx::AnalysisDataStorage::startFrame(const gmx::AnalysisDataFrameHeader&) API error (bug): Out of bounds frame index For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` In the trajectory, there are positions and velocities (no forces), both saved every 0.2 ps (i.e. every 200 timesteps) as confirmed by `gmx check`: ```nohighlight Item #frames Timestep (ps) Step 250001 0.2 Time 250001 0.2 Lambda 250001 0.2 Coords 250001 0.2 Velocities 250001 0.2 Forces 0 Box 250001 0.2 ``` I also tried different types of the selection (different groups, `-seltype atom`) with the same results. Do you have an idea, whether it is a misusage/not implemented feature or a bug? Best, Andreas ---
**Author:** ![apoma](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/apoma/32/1819_2.png) [@apoma](https://gromacs.bioexcel.eu/u/apoma)\ **Post date:** [November 16, 2022, 9:58pm UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/6 "2022-11-16T21:58:18Z")
Hi, Did you manage to get the Velocities? I am reporting also something similar with gmx trajectory. Take a look at [GMX trjconv does not print forces and velocities from trajectory trr file](https://gromacs.bioexcel.eu/t/gmx-trjconv-does-not-print-forces-and-velocities-from-trajectory-trr-file/5205) If you managed to fix this, I will appreciate any hint. best, Adolfo ---
**Author:** ![apoma](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/apoma/32/1819_2.png) [@apoma](https://gromacs.bioexcel.eu/u/apoma)\ **Post date:** [November 17, 2022, 10:51am UTC](https://gromacs.bioexcel.eu/t/gmx-trajectory-not-extracting-force-or-velocities/3087/7 "2022-11-17T10:51:30Z")
it seem to be a problem with **gmx trajectory** with flag **-ov -of** and it requires someone to check It out. Alternatively if you are not interested in -select, you can use the simple > gmx g\_traj with flags -ov -of with same flags and it works for me, as long as your trr file has save the velocities and forces (nstxout, nstvout, nstfout). cheers, Adolfo