[gmx-users] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

[Anh Vo]

Hi All,

I’m currently running GROMACS to simulate a simple phospholipid bilayer
membrane (POPC) under deformation.

1. For production step, GROMACS does not allow me to use Nose-Hoover
barostat for pressure coupling, I can only choose among Berendsen,
Parrinello-Rahman, Isotropic or MTTK options.

What are the differences between *Parrinello-Rahman, Nose-Hoover and MTTK?*
Nose-Hoover can be used for temperature coupling, but not for pressure
coupling. Why is that?

2. I'm not very clear what is constraints? And what are the differences
between LINCS and SHAKE constraint algorithm?

3. What does "refcoord_scaling" do in pressure coupling?

Thank you very much for sharing your time.

Best regards,
Anh Vo