[gmx-users] Pressure Question

[Johnny Lu]

That post in the amber mailing list was quite interesting. May be using a
weak berendsen thermostat in NVT is fine for them. Thanks for sharing that.

On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> I was not offended by the suggestion. With a sufficiently large number of
> water molecules, the protein would behave in the same way, under all three
> ensembles.
> Barostat and thermostat are artificial in some way. At least, even the
> diffusion coefficient is different in a force field paper that used both
> NVE and NVT. Langevin thermostat destroys some momentum transfer.
>
> This is my first paper, and I don't know if the reviewer will be fine if I
> report that my simulation has an average pressure of 11 bar with error 0.5
> bar.
>
>
> On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane <
> stephane.teletchea at univ-nantes.fr> wrote:
>
>> Le 06/11/2014 06:16, Antonio Baptista a écrit :
>>
>>>
>>> In particular, the virial-based "instantaneous pressure" (call it P')
>>> computed in simulations has its ensemble average equal to the thermodynamic
>>> pressure P (check any good book on molecular simulation). But, as others
>>> already pointed out, this P' is well-known to show extremelly large
>>> fluctuations, meaning that its average computed from the simulation has
>>> usually a very large statistical spread. In other words, although the
>>> ensemble average of P' is strictly equal to P, its simulation average is a
>>> random variable that often shows large deviations from P (especially for
>>> short simulations). To get an idea of what is an acceptable error for the
>>> average of P', you may look at its distribution histogram in the NPT
>>> simulation.
>>>
>>
>> Dear Antonio,
>>
>> Sorry if my message sound "aggressive" when I talked about "totally
>> irrevelevant", I will clarify my thoughts.
>>
>> From a theoretical point of view, you are right, each ensemble is
>> accessible.
>>
>> From a biological point of view, though, the concept of fixing the volume
>> is less reasonable:
>> we live at constant pressure and temperature, and also at tighly
>> controlled pH, and salt concentrations.
>>
>> The volume varies though, as you feel it when the weather is getting hot
>> or cold.
>>
>> My point was exactly what your are telling in a more formal way than me:
>> "this P' is well-known to show extremely large fluctuations"
>>
>> Well, digging a bit more on my "feeling", I also found opposite arguments
>> on the AMBER mailing list,
>> like here: http://archive.ambermd.org/201103/0431.html
>>
>> So I'll got back again on my research and adjust my "mind" on the actual
>> bleeding edge simulations
>> taking into account all the recent code and force fields progresses.
>>
>> Best,
>>
>> Stéphane
>>
>> --
>> Team Protein Design In Silico
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>> UFR Sciences et Techniques,
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>>
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>
>