gmx convert-tpr

User discussions
1

Dear Gromacs Community

I am working with simulations in GROMACS and I have a question regarding the usefulness of the gmx convert-tpr tool. I have reviewed the documentation, but I would like to better understand in which scenarios it is advisable to use this command and what its main function is in modifying .tpr files.

For example, I would like to know if it is useful for adjusting parameters in an already created input file without having to regenerate everything from scratch, or if it has any other specific application in molecular dynamics simulations.

I would greatly appreciate any guidance or suggestions you can give me on this matter.

Best regards

Note: I am attaching part of the script on how I run the simulations:

mpirun gmx_mpi grompp -f “{prod_prefix}.mdp" -o "{new}.tpr” -c “{old}.gro" -t "{old}.cpt” -p topol.top -n index.ndx

mpirun -np “SLURM_NTASKS" gmx_mpi mdrun -cpi "{ new}.cpt” -s “{new}.tpr" -dlb yes -notunepme -deffnm "{istep}”

2

I would say that its main use is to extend simulations, i.e., change the number of steps.

3

Dear @ruffovalla

As per the documentation, you have three main cases.
i) The first is simply to modify the length of the simulation. Example: did you request 100ns and the simulations finished but you want 100 more? Then just gmx convert-tpr -s old.tpr -o new.tpr -extend 100000.
ii) To ‘reduce’ your .tpr, mostly for analysis. Example: you have a long trajectory of a protein in water, which occupies a lot of memory, and you strip the water from the trajectory to handle it better in your analysis which focuses only on the protein. Your new trajectory will contain less atoms than the original one. If you want to use a tool in GROMACS which requires the .tpr file, you will get errors as GROMACS cannot understand why your trajectory has N atoms while your .tpr has N+num_waters atoms. So you gmx convert-tpr -s old.tpr -o new.tpr -n index.ndx and you output a new tpr file that contains only the protein to use for your analysis tool (and nothing else, as this tpr is ‘fake’, you can’t really use it to run sims in general).
iii) Another purpose similar to point ii), so changing some parameters to apply some specific method. I don’t have an example here as I never really used it for this purpose.

In practice, you will use it 99% of the time to extend the simulation time, at least in my experience. If you change other parameters in the .mdp file (e.g., temperature, cut-offs, etc) you will have to go through gmx grompp again to produce a new tpr file.

4

I understand!! Thank you very much!!