# Backmapping CG to AA

**URL:** <https://gromacs.bioexcel.eu/t/backmapping-cg-to-aa/13433>\
**Category:** User discussions\
**Created:** [May 3, 2026, 11:34am UTC](https://gromacs.bioexcel.eu/t/backmapping-cg-to-aa/13433 "2026-05-03T11:34:19Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Kapali](https://avatars.discourse-cdn.com/v4/letter/k/b4bc9f/32.png) [@Kapali](https://gromacs.bioexcel.eu/u/Kapali)\
**Post date:** [May 3, 2026, 11:34am UTC](https://gromacs.bioexcel.eu/t/backmapping-cg-to-aa/13433/1 "2026-05-03T11:34:19Z")

</div>

**GROMACS modification:** No

**Question:**

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

```auto
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:

```auto
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.