On Mon, 16 Apr 2007 09:40:58 +0200
lorix <[EMAIL PROTECTED]> 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
loris...
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list.
Use the www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
Hi Lorix,
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.
greetings
Jelger
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
