[gmx-users] pressure, pressure coupling, md-simulation

[Mark Abraham]

Carsten Baldauf wrote:
> hi all//
> I am running simulations of two peptides in a spc-water box. when i take 
> a look on the pressur using g_energy i get a for me surprising result 
> [see table attached at the end].
> my paramters in the mdp-file:
> Pcoupl                   = Berendsen
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> i would have expected values that vary around 1, but not that strong ...
> any comments?

Wild fluctuation of pressure is a standard observation made by people 
new to MD simulations - we see a few inquiries on this list each year 
:-) Negative pressure just means the system has a tendency to contract, 
positive to expand. Pressure regulation is a negative-feedback 
algorithm, so you will see variation of the sign of delta pressure/delta 
time. Further, it is actually not trivial to define a meaningful 
instantaneous pressure - the numbers you are used to thinking about are 
time-averaged quantities, and this makes sense if you think about the 
usual sort of kinetic derivation of the ideal gas law. The magnitude of 
these fluctuations is surprising, but entirely normal.

Mark