Creating a topol.tpr file for plumed

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1

GROMACS version:
GROMACS modification: Yes/No
Here post your question How can I create a topol.tpr file to use in a Plumed metadynamics simulation from my own pdb file? Alternatively is it possible to edit a topol.tpr file so that the cut off scheme can be changed?

2

Hi,
I am not familiar with plumed implementation, but in general tpr files are created by the tool gmx grompp (gmx grompp — GROMACS 2021.2 documentation). To use gmx grompp one need a coordinate file, a topology file and a md parameter file (.mdp). To generate topology file from a pdb file one can use gmx pdb2gmx .
For the options in mdp file you can see the setting in the current (old) tpr file by using gmx dump gmx dump — GROMACS 2021.2 documentation
Best regards
Alessandra

3

Thank you so much!