CpHMD Simulation Analysis

User discussions
1

GROMACS version: 2023.3

HI,
I am currently working on a Constant pH Molecular Dynamics simulation project and have successfully completed the simulation phase. The simulation has generated .xtc files, but I am unsure whether it should also produce a .gro file upon completion. Could you please confirm if the absence of a .gro file indicates an incomplete simulation?

Additionally, as I prepare to initiate the analysis phase using MDAnalysis, I have come across references to a script titled analysis_titration.py, which reportedly includes all necessary analyses for CpHMD simulations. However, I have been unable to locate this script in the GitHub repository. Would you be able to provide access to this script or direct me to where I can find it?

Thanks in advance.
Heshine

2

You should normal get a confout.gro file upon completion. But you can see in the md.log file how many steps the simulation performed.

You second question is about MDAnalysis, which is not a question for this forum. But I would imagine that such a script is specific for the package used to perform the CpHMD simulation, so I don’t know if it will work for files produces by GROMACS (my guess is not).