GROMACS: Use Parrinello-Rahman barostat

[HanatoK]

New versions of GMX deprecate the use of Berendsen barostat.

This commit should solve the problem mentioned in #96.

[fhh2626]

PR barostat is not very stable in equilibration. Should we use MC barostat?

[HanatoK]

@fhh2626
Have you tried it? I will run the p41 example with the Parrinello-Rahman barostat to see if it is stable.

OK. I see the warning in step 7. I will look into a better solution.

[HanatoK]

I am testing the C-rescale, which supports both equilibration and production simulations. However, it requires GROMACS 2021 and above.

[fhh2626]

@fhh2626 Have you tried it? I will run the p41 example with the Parrinello-Rahman barostat to see if it is stable.

OK. I see the warning in step 7. I will look into a better solution.

Yes. I tested the PR barostat previously and it did not stable in the initial stage of equilibration.

[fhh2626]

So should we?

[HanatoK]

So should we?

No. I incline to use C-rescale and will change the code. The only problem is that it requires GROMACS 2021. The simulation is still running, and I will see if the results are correct.

[HanatoK]

@fhh2626
I change the default pcoupl to C-rescale, and the TPR files can be generated without errors. Simulations are stable and not crashed. Trajectories look good. The only problem is that the binding free energy (from Abl kinase SH3:p41) still cannot match the result from NAMD, which I remember it is the same as what I have tried before.

[fhh2626]

What do you mean "The only problem is that the binding free energy (from Abl kinase SH3:p41) still cannot match the result from NAMD"? In my previous test everything seemed good.

[HanatoK]

What do you mean "The only problem is that the binding free energy (from Abl kinase SH3:p41) still cannot match the result from NAMD"? In my previous test everything seemed good.

See the attached screenshot. The results are quite different from those from NAMD simulations.

[HanatoK]

@fhh2626
I am going to run the old version (pcoupl = Berendsen) again but with -maxwarn 1 to suppress the warning, and to see if the binding free energy matches the NAMD result.

[fhh2626]

Did you use a stratification strategy for steps 1, 7 and 8? The use of 3, 5, 3 windows respectively for the three steps guarantees a good convergence of the simulations.

[HanatoK]

No, but I will try it.

[fhh2626]

This is good for me. Can we merge this PR now?

[HanatoK]

@fhh2626
OK. I think C-rescale is at least better than Berendsen.