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...
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