[gmx-users] NVT + frozen groups

[Erik Lindahl]

Valentin Gogonea wrote:
> Hi gromacs users,
> 
> If I understood correctly, a system containing frozen groups must be 
> simulated as NVT (with no pressure coupling) Is this correct?

Well, the frozen atom coordinates won't be updated or scaled with
the box when everything else scales in the pressure coupling. If that's 
OK with you, I don't think there should be any problem :-)


> I made a 200 ps simulation of myoglobin in water (no frozen groups) 
> without pressure coupling. The pressure starts at 63 bar and drops at 
> -500 bar. Do these pressure number have any meaning in a NVT simulation?

Yes, it is the pressure in your system, and it is quite reasonable that
it gets lower when the particles equilibrate. It won't affect the motion
of the particles (or the box size) unless you turn on pressure scaling, 
though.

It's exactly the same thing as the temperature in an NVE simulation; it
is still well defined and it might change during the simulation, but it
will not affect the dynamics unless you turn on temperature coupling (NVT).

Cheers,

Erik