GROMACS version: 2019.3
GROMACS modification: No
Dear users,
I would like to use the gmx convert-tpr tool to edit the .tpr file. The idea is from the original MD trajectory file I select only one part of the system with gmx trjconv. However, the analysis tool that I’m using (is not any gromacs tool) gives an error because the number of atoms in topology file (.tpr) doesn’t match the number of atoms in the trajectory (.xtc). So I use the gmx convert-tpr tool to select the same atoms that I choose in the gmx trjconv in order to get the necessary match between the correct atoms and the number of atoms as in the .xtc file. The analysis tool seems to work with this approach and no apparent issue was raised. My question is concerned with the GROMACS documentation of gmx convert-tpr tool where there is this warning: " WARNING: this .tpx file is not fully functional " . This warning appears also in the more recent GROMACS versions. Is the tool doing correctly what I’m asking him to do? Is there bugs to be fixed in this tool? Or is this a warning concerning only to the fact that the new .tpr file might not be functional to run a simulation with gmx mdrun?
Thank you in advance.
Yes, this is advising to not use this partial tpr file for simulation. The subset feature is designed to be used with analysis tool as you describe with gromacs tool.
It is probably also fine with external tools, but you might need to be a little bit cautious depending on what it does - if it only uses the coordinates of the atoms and/or charges and masses, it should be okay.