Backmapping CG to AA

User discussions
1

GROMACS modification: No

Question:

I am trying to convert a coarse-grained structure to an atomistic representation using CG2AT with the command:

cg2at -c last_frame_clean.gro

I selected the following parameters:

  • Forcefield: charmm36-jul2020-updated

  • Fragment library: martini_2-2_charmm36

  • Water model: TIP3P

The conversion starts successfully and prints:

Completed initial conversion of PROTEIN
Running pdb2gmx/minimisation on 200 molecules. Percentage complete: 0.0 %

However, the progress remains at 0.0% for a long time, and after some time, no files appear to be updated. It is unclear whether the process is still running or has stalled.

Questions:

  1. Is this behavior expected for systems with ~200 molecules, or does it indicate a problem?

  2. How can I verify whether the process is still running or stuck?

  3. Is there a way to speed up this step (e.g., parallelization or reducing workload)?

  4. Could this be related to an incorrect fragment library (e.g., Martini 2 vs Martini 3 mismatch)?

Any guidance would be appreciated.