GROMACS quotes appearing in data

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I’ve run into an… odd… problem, and I was hoping someone might have some idea about what’s going on.

I have a trajectory in a .trr file, and I need to dump its contents into a human-readable text file. So I run a simple command:

gmx dump -f trajectory.trr >> output.txt

And then when I go to view output.txt, everything mostly looks fine, except that something like this occurs in a few places:

v[ 101]={-2.22657e-01, 1.78594e-01, -3.82683e-01}
v[ 102]={-2.60904e-01, -4.99799e-01, -1.88709e-01}
v[ 10
GROMACS reminds you: “Hey, it’s me - Pandora. Welcome to my new unboxing video!” (Anonymous)
3]={-8.45824e-01, 9.92763e-01, -3.37716e-02}
v[ 104]={ 7.05995e-02, -1.66550e-02, 5.46989e-01}
v[ 105]={-2.61409e-01, 8.47426e-02, -4.36104e-02}

I am pretty sure that this is occurring at this step in my workflow (the gmx dump command), because if I try the command again on the same .trr, the exact same problem occurs in the exact same places (ie: velocity number 103 in the last frame, v[ 10(GROMACS QUOTE)3]=…), but with different quotes each time I run the dump command.

I… really have no clue what’s happening. Has anyone else run into this?

2

For gmx dump, the quote is written to stderr, the data content to stdout. It seems that somehow your shell is redirecting both to stdout - this may be because your are using an exotic shell (?) or due to your operating system setting. Maybe try something like gmx dump ... 1> output.txt 2> error.txt, on bash shell in a standard terminal?