# Problems with generating self contained topology file (necessary for partial tempering with plumed)

**URL:** <https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708>\
**Category:** User discussions\
**Tags:** grompp\
**Created:** [September 29, 2025, 11:45am UTC](https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708 "2025-09-29T11:45:35Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Blue](https://avatars.discourse-cdn.com/v4/letter/b/3bc359/32.png) [@Blue](https://gromacs.bioexcel.eu/u/Blue)\
**Post date:** [September 29, 2025, 11:45am UTC](https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708/1 "2025-09-29T11:45:35Z")

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GROMACS version: 2025.3  
GROMACS modification: Yes (patched with PLUMED 2.9.4)  
Here post your question

Hello, it’s me again with another question.

I want to set up HREX MD simulations with plumed. For that, I need a self contained topology file. My partial tempering with plumed fails (ERROR: params not found 5 18\_ 20 21 9 CT N H) and I believe that is due to the generation of my self contained topology file. The tutorial I am following tells me to use gmx\_mpi grompp -p topol.top -pp processed.top, but GROMACS then gives me an error because it requires -c and -f. So I ran this instead: gmx\_mpi grompp -f tempering.mdp -c npt\_5.gro -p topol\_prod.top -pp processed.top -o dummy.tpr -r npt\_5.gro -maxwarn 2  
with a very small tempering.mdp file:  
; minimal mdp for preprocessing only  
integrator = md  
dt = 0.002  
nsteps = 10  
; don’t define POSRES here  
; keep other settings simple and valid  
constraints = h-bonds  
coulombtype = PME  
rcoulomb = 1.0  
rvdw = 1.0  
pbc = xyz  
Aditionally, I had used positional restraints during the NPT run (gradually reducing from 1000 to 5) and don’t want to use them here anymore, so I commented all the lines pointing to restraints out in the topol.top file.

Is this the way to go? How can I check whether my processed.top is really fully self contained and does not contain some weird restraints or other artifacts that I do not want? Could the reason for the error be that the angletype CT N H does not exist?

Sorry for all the questions, I have spent a long time trying to make sense of everything and am more confused than before.

Any help is greatly appreciated!

Best wishes,

Blue

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<div class="post-metadata">

**Author:** ![Blue](https://avatars.discourse-cdn.com/v4/letter/b/3bc359/32.png) [@Blue](https://gromacs.bioexcel.eu/u/Blue)\
**Post date:** [September 29, 2025, 1:16pm UTC](https://gromacs.bioexcel.eu/t/problems-with-generating-self-contained-topology-file-necessary-for-partial-tempering-with-plumed/12708/2 "2025-09-29T13:16:40Z")

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Nevermind, I solved it.