[gmx-users] Pressure Question

[Téletchéa Stéphane]

Le 04/11/2014 18:00, Johnny Lu a écrit :
> Hi.
>
> If my NVT simulation of a protein in 30k molecules of water has a pressure
> of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
> distribution of conformations) change enough that the mechanism inferred
> from this simulation be significantly more unreliable than the mechanism
> inferred from a 1 bar simulation? (Will the reviewers cut my paper into
> ribbons?)
>
> Thanks again.

Hi,

Considering only your "NVT" parameters for your simulation,
I would consider it totally irrelevant to talk about "pressure" where 
your constrain the volume.
This value or any other one has not really a meaning in this situation, 
and I seen
many variations in the pressure value in this microcanonical ensemble 
without paying too much
attention on it.

In an "NPT" simulation, then you should be able to find back a normal 1 
bar simulation I think.

Do you have any reason to do first an NPT simulation, and "then" an NVT one?
I would personally let the system equilibrate in NVT, then swith to the 
more natural NPT,
provided actual code and force fields are now good enough in this ensemble.

Best,

Stéphane

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