Hi Berk and Jelger,
Thanks for your comments...
Yes I equilibrated the system with Berendsen thermostat and barostat for
100ps and 200 ps and then switched them off.
I thought that the coupling could have an influence in the final
trajectory, because of the atom velocities scaling (?).
Why does not make sense to run NVE after NPT?
The two systems (15000 and 40000 atoms) I am simulating at NVE both show
increasing total energy:
The first system had -154442 kJ mol^-1 as average for the 7-207 psec NPT
equilibration and -168837 kJ mol^-1 as average value for 1500-2000 ps of
NVE.
The second system had -445679 kJ mol^-1 as average for the 14-114 psec
NPT equilibration and -465630 kJ mol^-1 as average for the 300-600 ps of
NVE equilibration.
greetings
loris...
Berk Hess wrote:
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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