GMX Trajectory not extracting force or velocities

User discussions
1

GROMACS version: 2021.3
GROMACS modification: Yes

I have these enabled in my md file:

nstxout                = 500 
nstvout                = 500
nstfout                 = 500

but when I use:

gmx trajectory

I could only extract the position but not the velocities and forces. How to extract forces and velocities from my trajectory files?

2

What does gmx check tell you about the contents of the trajectory? What was your exact gmx trajectory command?

3

This is what appears after: gmx check -f md.trr -rmsd

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
4

And what was your gmx trajectory command?

5

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:

-------------------------------------------------------
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:

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

6

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
If you managed to fix this, I will appreciate any hint.
best,
Adolfo

7

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