Hi, I'm working on Gromacs on HPC to run MD simulations. I tried combining individual files from step 5, which is the MD production step, using the gmx trjcat command so that I could post-process the simulation.
The problem is that the files start at the same time or time frame? We got suspicious because the resulting file of the gmx trjcat command is the same file size as the other .xtc files, instead of resulting in a file that has the file size of all combined .xtc files. Also, the resulting file of the gmx trjconv command is the same size as the resulting file of the gmx trjcat command.
Attach below are relevant screenshots of what happened to my post-processing attempt:
You can do it two ways:
1) Adding "-settime" (to manually specify the start time of each file) or "-cat" (to simply concatenate all files) to gmx trjcat;
2) Loading sequentially to VMD and saving the concatenated file.
Hi. Use the following command to solve the problem:
gmx trjcat -f 1.xtc 2.xtc -o 3.xtc -cat –settime
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