From: lorix <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: [gmx-users] on NVE and pressure
Date: Mon, 16 Apr 2007 09:40:58 +0200
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
loris...
You have equilibrated your modified conformation at 300 K and 1 bar?
Then it does not make sense to use NVE.
It only makes sense to use NVE when you have some ultra fast process
that somehow puts energy into your system and you have a way
to describe this energy transfer process reasonably accurately.
You can not judge if your ensemble is ok just by looking at the temperature.
In NVE you should make sure the total energy is reasonably conserved.
Berk.
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