[gmx-users] NVT + frozen groups

Valentin Gogonea v.gogonea at csuohio.edu
Wed Jul 10 01:39:42 CEST 2002

Thanks Erik for you quick answer.

Does it make sense to make NPT simulations with frozen groups? I mean if 
the coordinates of the frozen atoms are not scaled what happen with the 
bonds between atoms in the moving part and those in the frozen part?

In a hypothetical situation that the moving region is totally buried in 
the frozen one, how does the pressure coupling works? It seems to me 
that the box size cannot be adjusted in this case because the moving 
part is wrapped in a hard wall. Am I wrong?

Thank you for your comments.


On Tuesday, July 9, 2002, at 07:27 PM, Erik Lindahl wrote:

> 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

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