Dear gromacs users,
I am using an mdp file obtained from another source, however it does not have pbc = xyz entry in the mdp file. But I see in the mdout.mdp and md.log file shows pbc=xyz, does this mean gromacs by default considers pbc=xyz in all three directions even if the option is not specified in the mdp file? Any help would be much appreciated, thank you
Yes, the automatically generated mdout.mdp would show the full setting.
You can also have a look at Molecular dynamics parameters (.mdp options) - GROMACS 2024.3 documentation to see which option is listed first. “Default values are given in parentheses, or listed first among choices. The first option in the list is always the default option.”
Thank you for your response, however for pbc in mdp file, there is no value given in parenthesis. But if I don’t provide pbc option, I can see that the mdout.mdp and the md.log file contains pbc=xyz option.
Thank you for your response.
The first option in Molecular dynamics parameters (.mdp options) - GROMACS 2024.3 documentation is xyz, and “the first option in the list is always the default option”.