[gmx-users] Scale down/ up velocities when coupling temperature and pressure?

[Yun Shi]

Hi all,

I am just wondering about how GROMACS works when coupling temperature and
pressure.

Assuming the simplest coupling method, like Berendsen, does GROMACS just
scale down/ up kinetic energy (KE) for each particle in the system, such as
KE1/KE2 = T1/T2 ? Similarly for pressure, KE1/KE2 = P1/P2? So GROMACS
scales the square root of velocities for every particle after each time
step?


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BTW, the number of degrees of freedom = 3N - Nc - Ncom according to the
manual. For conventional MD, is Nc equal to the total number of constrained
bonds (like all bonds in gromos ff, and all bonds involving hydrogens in
amber99sb ff)?

Thanks for any explanation.

Yun
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