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

Blue
Mon, 29 Sep 2025 11:45:35 +0000
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GROMACS version: 2025.3
GROMACS modification: Yes (patched with PLUMED 2.9.4)
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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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