[gmx-users] Pressure Question

[Johnny Lu]

Well... I finally have to accept that I really need NVE. Some forum posts
suggested to run NPT, then NVT, and finally NVE.

For ideal gas law, if we fix the number of molecules and the temperature,
then fixing the volume at different value means changing the pressure.
So, I guess pressure is still meaningful, if I have to decide the correct
volume to run the NVT simulation.

For a large number of ideal gas molecules, averages of all thermodynamic
variables should be defined, regardless of which three of them is fixed or
which ensemble do I choose to represent the state.
For a small number of molecules, the distribution of the thermodynamic
variables should still have a definition (so, the average and the
distribution of pressure is still meaningful).

For a protein simulation, it still has a partition function, and equation
of state.

I mainly want to know how much error in pressure (deviation from 1 bar) is
acceptable.

On Wed, Nov 5, 2014 at 2:35 PM, Téletchéa Stéphane <
stephane.teletchea at univ-nantes.fr> wrote:

> 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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