I do have a question.
I simulated a molecules for 100ns and when I wanted to do RMSD and Gyration calculations from it, I got this error
“Reading frame 32000 time 63926.000 Floating point exception (core dumped)”
So if I am not mistaken this frame there is corrupt and therefore leads to problems.
Now, I am asking myself whether it is possible to just “skip” the frame somehow?
While preparing the no PBC-file i used trjcov and -dump 63926 but that obviously just removed every frame after that one :/
Is there a skip option or does anybody has an idea what I can do, besides simulating a new dataset?
In the past we used a combination of gmx trjcat and gmx_rescue64 to reassemble a trajectory with bad frames excised. A long time ago one of my students wrote a simple script to semi-automate the process and put it up at GitHub - Becksteinlab/gmx_first_aid: A command line utility intended to assist in recovering data from corrupted gromacs trajectories. — sorry, there’s no documentation for the first-aid.sh script beyond reading the script itself (and the script also needs to be adapted) but you might get an idea how to go about it. The source code for gmx_rescue64 is also in this repo.
I can’t help much more than pointing you to the repo. I hope you can make it work.