[gmx-users] on NVE and pressure
H.J.Risselada at rug.nl
Mon Apr 16 11:31:09 CEST 2007
On Mon, 16 Apr 2007 09:40:58 +0200
lorix <Loris.Moretti at pharm.unige.ch> wrote:
> Hi everybody,
> I am simulating a protein (approximately 5000 atoms) in
>water (35000 atoms). The protein is out of a
>thermodynamic equilibrium because I modified a
>crystallographic structure of one of its conformation
>(which showed stability with MD). Thus, my aim would be
>to let the system evolve to a new equilibrium. I am
>expecting a conformation for the protein smaller in size
>than the starting point.
> I had several simulations with Temperature and pressure
>coupling and now I have decided to go for NVE (after a
>prior equilibration with TP controls for 300 K and 1 bar)
>, the decision is mainly because I do not want to affect
>the evolution of atom velocities during the simulation.
> With the NVE ensemble after 2 nsec I have an average
> value for Temperature about 285 K while the Pressure
>average value is around -230 bar. The temperature is
>clearly fine. While the big negative value for pressure
>is meaning that the system wants to contract if I
>understood correctly ? How does this pressure affect the
>system? Have I to consider the pressure just like a
>tendency of the system either to contract or to expand?
> thanks for any suggestion
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Don't worry ;-)
Because actually there is no thermodynamic sense of
defining pressure in a NVE ensemble at all. In the
thermodynamic limit pressure is defined as: -(dE/dV)=p,
while in the microcanonical ensemble E,V are constant.
The definition of pressure in Gromacs arises from
mathematically constructed stresses on a nanoscopic
system. So when doing NVE, you still get your numbers but
puristically speaking it doesn't mean much.
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