Error in NPT Equilibration for Protein Ligand Complex MD Tutorial

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GROMACS version: 2023.3
GROMACS modification: No

I encountered an issue when in the NPT Equilibration phase of the Protein Ligand Complex tutorial on their website (Protein-Ligand Complex).

The error read:

WARNING 1 [file npt.mdp]:
The Berendsen barostat does not generate any strictly correct ensemble,
and should not be used for new production simulations (in our opinion).
We recommend using the C-rescale barostat instead.

So, I went over to the following line in my npt.mdp file, and changed it from this:
tcoupl = V-rescale ; modified Berendsen thermostat

to this:
tcoupl = C-rescale ; modified Berendsen thermostat

I received another error by running the same command as before (gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr).

The new error read:

ERROR 1 [file npt.mdp, line 49]:
Invalid enum ‘C-rescale’ for variable tcoupl, using ‘No’
Next time, use one of: ‘No’ ‘Berendsen’ ‘Nose-Hoover’ ‘yes’ ‘Andersen’
‘Andersen-massive’ ‘V-rescale’

How do I solve this issue so that I can move onto the next step in the tutorial which is performing an mdrun on npt?

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You have used NO YES and added the C-rescale or v-scale- share the mdp file

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Dear @AmeerM0625

Re-read the error! :) The warning is complaining about the BAROSTAT, not the thermostat.

The c-rescale is a barostat and cannot be used as a thermostat. What GROMACS is saying is that you are using an unknown thermostat, so it is switching to tcoupl = No. As you can see, among the suggestions in the error line there is the tcoupl=v-rescale, so your previous thermostat was already correct (and, arguably, the best choice at the moment).

You were using probably Berendsen as the pressure coupling type, which is not the best, and GROMACS is suggesting you to switch to the c-rescale. Just set pcoupl=c-rescale and you are good to go!

5

Thank you very much for you response @obZehn !

You are right, my pcoupl variable was set to Berendsen and upon changing it to C-rescale the issue was resolved when I ran my command.