Grompp log file

GROMACS version: 2021.3
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I typically use a bash script to run multiple mdp files (energy minimization, equilibration, production run) and pass “-maxwarn 2” to grompp so that the simulations can continue. While most of the warnings and notes that grompp spits are harmless in my simulations, I would still like to see those after the simulations have ended. Is there a way to export these in a log file?

An obvious way is to scroll in the console window but there seems to be a character limit and only the last few hundred lines are shown thus necessitating the need for a log file.


You like to live dangerously, don’t you? :) Warnings are not, in fact, “harmless” as they are raised when there are issues of incompatibility or likely physical instability. About the harmless instance I can think of is naming mismatches, but these should be rare. Tread lightly with allowing your grompp commands to bypass not 1, but 2, potential problems.

Use the standard Linux tee command to duplicate stdout to a file.

Thanks Justin for the reply.

The “harmless” means warnings like Parinello- Rahman and position restraints incompatibility as grompp spits but these are otherwise acceptable in properly equilibrated systems. Or, like when rlist is automatically changed based on other settings in the mdp.

Thanks for the pointer to the tee command.